TY - JOUR A1 - Ma, Jie A1 - Gulbins, Erich A1 - Edwards, Michael J. A1 - Caldwell, Charles C. A1 - Fraunholz, Martin A1 - Becker, Katrin Anne T1 - Staphylococcus aureus α-toxin induces inflammatory cytokines via lysosomal acid sphingomyelinase and ceramides JF - Cellular Physiology and Biochemistry N2 - Staphylococcus aureus (S. aureus) infections are a major clinical problem and range from mild skin and soft-tissue infections to severe and even lethal infections such as pneumonia, endocarditis, sepsis, osteomyelitis, and toxic shock syndrome. Toxins that are released from S. aureus mediate many of these effects. Here, we aimed to identify molecular mechanisms how α-toxin, a major S. aureus toxin, induces inflammation. Methods: Macrophages were isolated from the bone marrow of wildtype and acid sphingomyelinase-deficient mice, stimulated with S. aureus α-toxin and activation of the acid sphingomyelinase was quantified. The subcellular formation of ceramides was determined by confocal microscopy. Release of cathepsins from lysosomes, activation of inflammasome proteins and formation of Interleukin-1β (IL-1β) and Tumor Necrosis Factor-α (TNF-α) were analyzed by western blotting, confocal microscopy and ELISA. Results: We demonstrate that S. aureus α-toxin activates the acid sphingomyelinase in ex vivo macrophages and triggers a release of ceramides. Ceramides induced by S. aureus α-toxin localize to lysosomes and mediate a release of cathepsin B and D from lysosomes into the cytoplasm. Cytosolic cathepsin B forms a complex with Nlrc4. Treatment of macrophages with α-toxin induces the formation of IL-1β and TNF-α. These events are reduced or abrogated, respectively, in cells lacking the acid sphingomyelinase and upon treatment of macrophages with amitriptyline, a functional inhibitor of acid sphingomyelinase. Pharmacological inhibition of cathepsin B prevented activation of the inflammasome measured as release of IL-1β, while the formation of TNF-α was independent of cathepsin B. Conclusion: We demonstrate a novel mechanism how bacterial toxins activate the inflammasome and mediate the formation and release of cytokines: S. aureus α-toxin triggers an activation of the acid sphingomyelinase and a release of ceramides resulting in the release of lysosomal cathepsin B and formation of pro-inflammatory cytokines. KW - Staphylococcus aureus KW - sphingomyelinase KW - ceramide KW - toxins KW - macrophages KW - cytokines Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181481 VL - 43 IS - 6 ER - TY - JOUR A1 - Szklarczyk, Damian A1 - Morris, John H. A1 - Cook, Helen A1 - Kuhn, Michael A1 - Wyder, Stefan A1 - Simonovic, Milan A1 - Santos, Aalberto A1 - Doncheva, Nadezhda T. A1 - Roth, Alexander A1 - Bork, Peer A1 - Jensen, Lars J. A1 - von Mering, Christian T1 - The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible JF - Nucleic Acids Research N2 - A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein–protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein–protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/. KW - string database KW - quality control KW - proteins KW - cellular function Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181445 VL - 45 IS - D1 ER - TY - JOUR A1 - Rhee, Jae-Sung A1 - Choi, Beom-Soon A1 - Kim, Jaebum A1 - Kim, Bo-Mi A1 - Lee, Young-Mi A1 - Kim, Il-Chan A1 - Kanamori, Akira A1 - Choi, Ik-Young A1 - Schartl, Manfred A1 - Lee, Jae-Seong T1 - Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus JF - Scientific Reports N2 - The Kryptolebias marmoratus is unique because it is the only selffertilizing hermaphroditic vertebrate, known to date. It primarily reproduces by internal self-fertilization in a mixed ovary/testis gonad. Here, we report on a high-quality genome assembly for the K. marmoratus South Korea (SK) strain highlighting the diversity and distribution of transposable elements (TEs). We find that K. marmoratus genome maintains number and composition of TEs. This can be an important genomic attribute promoting genome recombination in this selfing fish, while, in addition to a mixed mating strategy, it may also represent a mechanism contributing to the evolutionary adaptation to ecological pressure of the species. Future work should help clarify this point further once genomic information is gathered for other taxa of the family Rivulidae that do not self-fertilize. We provide a valuable genome resource that highlights the potential impact of TEs on the genome evolution of a fish species with an uncommon life cycle. KW - ecological genetics KW - evolutionary genetics KW - ichthyology KW - Kryptolebias marmoratus Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181329 VL - 7 ER - TY - JOUR A1 - Mannucci, Ilaria A1 - Dang, Nghi D. P. A1 - Huber, Hannes A1 - Murry, Jaclyn B. A1 - Abramson, Jeff A1 - Althoff, Thorsten A1 - Banka, Siddharth A1 - Baynam, Gareth A1 - Bearden, David A1 - Beleza-Meireles, Ana A1 - Benke, Paul J. A1 - Berland, Siren A1 - Bierhals, Tatjana A1 - Bilan, Frederic A1 - Bindoff, Laurence A. A1 - Braathen, Geir Julius A1 - Busk, Øyvind L. A1 - Chenbhanich, Jirat A1 - Denecke, Jonas A1 - Escobar, Luis F. A1 - Estes, Caroline A1 - Fleischer, Julie A1 - Groepper, Daniel A1 - Haaxma, Charlotte A. A1 - Hempel, Maja A1 - Holler-Managan, Yolanda A1 - Houge, Gunnar A1 - Jackson, Adam A1 - Kellogg, Laura A1 - Keren, Boris A1 - Kiraly-Borri, Catherine A1 - Kraus, Cornelia A1 - Kubisch, Christian A1 - Le Guyader, Gwenael A1 - Ljungblad, Ulf W. A1 - Brenman, Leslie Manace A1 - Martinez-Agosto, Julian A. A1 - Might, Matthew A1 - Miller, David T. A1 - Minks, Kelly Q. A1 - Moghaddam, Billur A1 - Nava, Caroline A1 - Nelson, Stanley F. A1 - Parant, John M. A1 - Prescott, Trine A1 - Rajabi, Farrah A1 - Randrianaivo, Hanitra A1 - Reiter, Simone F. A1 - Schuurs-Hoeijmakers, Janneke A1 - Shieh, Perry B. A1 - Slavotinek, Anne A1 - Smithson, Sarah A1 - Stegmann, Alexander P. A. A1 - Tomczak, Kinga A1 - Tveten, Kristian A1 - Wang, Jun A1 - Whitlock, Jordan H. A1 - Zweier, Christiane A1 - McWalter, Kirsty A1 - Juusola, Jane A1 - Quintero-Rivera, Fabiola A1 - Fischer, Utz A1 - Yeo, Nan Cher A1 - Kreienkamp, Hans-Jürgen A1 - Lessel, Davor T1 - Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders JF - Genome Medicine N2 - Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-306477 VL - 13 ER - TY - JOUR A1 - Maas, Bea A1 - Brandl, Manuela A1 - Hussain, Raja Imran A1 - Frank, Thomas A1 - Zulka, Klaus Peter A1 - Rabl, Dominik A1 - Walcher, Ronnie A1 - Moser, Dietmar T1 - Functional traits driving pollinator and predator responses to newly established grassland strips in agricultural landscapes JF - Journal of Applied Ecology N2 - Agricultural biodiversity and associated ecosystem functions are declining at alarming rates due to widespread land use intensification. They can only be maintained through targeted landscape management that supports species with different habitat preferences, dispersal capacities and other functional traits that determine their survival. However, we need better understanding whether short-term measures can already improve functional diversity in European agroecosystems. We investigated spatio-temporal responses of bees (solitary bees, bumblebees and honey bees), hoverflies, carabid beetles and spiders to newly established grassland strips in Lower Austria over 3 years, and along a distance gradient to old grasslands. Specifically, we asked if new grasslands, compared to old grasslands and cereal fields, serve as temporal dispersal habitat or corridor, and how species-specific traits affect dispersal patterns. Using a trait-based functional diversity approach, we investigated year and distance effects for nine selected key traits per taxon (e.g. body size, feeding guild and habitat preferences). Our results show that the functional diversity of predators and pollinators (i.e. functional richness and evenness), as well as community-weighted means of selected key traits in new grasslands significantly differed from adjacent cereal fields, but only slowly adjusted to adjacent old grasslands. These effects significantly decreased with increasing distance to old grasslands for carabids and spiders, but not for mobile bees and hoverflies. Synthesis and applications. Over 3 years, newly established grassland strips supported larger sized and actively foraging/hunting species in the agricultural landscape. Adjacent crops likely benefit from such measures through enhanced functional diversity and related ecosystem services. However, our results also suggest that 3-year period is too short to enhance the occurrence of pollinators and epigeic predators in new grasslands. Agri-environment measures need to be complemented by the conservation of permanent habitats to effectively maintain species and functional diversity. Our findings should be acknowledged by European policy and agricultural decision makers for the design of more effective agri-environment schemes, taking into account trait-dependent species responses to land use change. KW - agri-environment schemes KW - Common Agricultural Policy KW - ecosystem services; KW - Europe KW - functional diversity analysis; KW - pollination KW - predation KW - trait-based management Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369992 VL - 58 ER - TY - JOUR A1 - Lu, Yuan A1 - Bierbach, David A1 - Ormanns, Jenny A1 - Warren, Wesley C. A1 - Walter, Ronald B. A1 - Schartl, Manfred T1 - Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly JF - Genome Research N2 - The Amazon molly is a unique clonal fish species that originated from an interspecies hybrid between Poecilia species P. mexicana and P. latipinna. It reproduces by gynogenesis, which eliminates paternal genomic contribution to offspring. An earlier study showed that Amazon molly shows biallelic expression for a large portion of the genome, leading to two main questions: (1) Are the allelic expression patterns from the initial hybridization event stabilized or changed during establishment of the asexual species and its further evolution? (2) Is allelic expression biased toward one parental allele a stochastic or adaptive process? To answer these questions, the allelic expression of P. formosa siblings was assessed to investigate intra- and inter-cohort allelic expression variability. For comparison, interspecies hybrids between P. mexicana and P. latipinna were produced in the laboratory to represent the P. formosa ancestor. We have identified inter-cohort and intra-cohort variation in parental allelic expression. The existence of inter-cohort divergence suggests functional P. formosa allelic expression patterns do not simply reflect the atavistic situation of the first interspecies hybrid but potentially result from long-term selection of transcriptional fitness. In addition, clonal fish show a transcriptional trend representing minimal intra-clonal variability in allelic expression patterns compared to the corresponding hybrids. The intra-clonal similarity in gene expression translates to sophisticated genetic functional regulation at the individuum level. These findings suggest the parental alleles inherited by P. formosa form tightly regulated genetic networks that lead to a stable transcriptomic landscape within clonal individuals. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369578 VL - 31 ER - TY - JOUR A1 - Loza-Valdes, Angel A1 - Mayer, Alexander E A1 - Kassouf, Toufic A1 - Trujillo-Viera, Jonathan A1 - Schmitz, Werner A1 - Dziaczkowski, Filip A1 - Leitges, Michael A1 - Schlosser, Andreas A1 - Sumara, Grzegorz T1 - A phosphoproteomic approach reveals that PKD3 controls PKA-mediated glucose and tyrosine metabolism JF - Life Science Alliance N2 - Members of the protein kinase D (PKD) family (PKD1, 2, and 3) integrate hormonal and nutritional inputs to regulate complex cellular metabolism. Despite the fact that a number of functions have been annotated to particular PKDs, their molecular targets are relatively poorly explored. PKD3 promotes insulin sensitivity and suppresses lipogenesis in the liver of animals fed a high-fat diet. However, its substrates are largely unknown. Here we applied proteomic approaches to determine PKD3 targets. We identified more than 300 putative targets of PKD3. Furthermore, biochemical analysis revealed that PKD3 regulates cAMP-dependent PKA activity, a master regulator of the hepatic response to glucagon and fasting. PKA regulates glucose, lipid, and amino acid metabolism in the liver, by targeting key enzymes in the respective processes. Among them the PKA targets phenylalanine hydroxylase (PAH) catalyzes the conversion of phenylalanine to tyrosine. Consistently, we showed that PKD3 is activated by glucagon and promotes glucose and tyrosine levels in hepatocytes. Therefore, our data indicate that PKD3 might play a role in the hepatic response to glucagon. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369560 VL - 4 ER - TY - JOUR A1 - Li, Yuanyue A1 - Kuhn, Michael A1 - Zukowska-Kasprzyk, Joanna A1 - Hennrich, Marco L. A1 - Kastritis, Panagiotis L. A1 - O'Reilly, Francis J. A1 - Phapale, Prasad A1 - Beck, Martin A1 - Gavin, Anne-Claude A1 - Bork, Peer T1 - Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum JF - PLOS ONE N2 - Protein–metabolite interactions play an important role in the cell’s metabolism and many methods have been developed to screen them in vitro. However, few methods can be applied at a large scale and not alter biological state. Here we describe a proteometabolomic approach, using chromatography to generate cell fractions which are then analyzed with mass spectrometry for both protein and metabolite identification. Integrating the proteomic and metabolomic analyses makes it possible to identify protein-bound metabolites. Applying the concept to the thermophilic fungus Chaetomium thermophilum, we predict 461 likely protein-metabolite interactions, most of them novel. As a proof of principle, we experimentally validate a predicted interaction between the ribosome and isopentenyl adenine. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-364299 VL - 16 ER - TY - JOUR A1 - Li, Ming A1 - Zhang, Rui A1 - Fan, Guangyi A1 - Xu, Wenteng A1 - Zhou, Qian A1 - Wang, Lei A1 - Li, Wensheng A1 - Pang, Zunfang A1 - Yu, Mengjun A1 - Liu, Qun A1 - Liu, Xin A1 - Schartl, Manfred A1 - Chen, Songlin T1 - Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus JF - Molecular Biology and Evolution N2 - Sex chromosomes are a peculiar constituent of the genome because the evolutionary forces that fix the primary sex-determining gene cause genic degeneration and accumulation of junk DNA in the heterogametic partner. One of the most spectacular phenomena in sex chromosome evolution is the occurrence of neo-Y chromosomes, which lead to X1X2Y sex-determining systems. Such neo-sex chromosomes are critical for understanding the processes of sex chromosome evolution because they rejuvenate their total gene content. We assembled the male and female genomes at the chromosome level of the spotted knifejaw (Oplegnathus punctatus), which has a cytogenetically recognized neo-Y chromosome. The full assembly and annotation of all three sex chromosomes allowed us to reconstruct their evolutionary history. Contrary to other neo-Y chromosomes, the fusion to X2 is quite ancient, estimated at 48 Ma. Despite its old age and being even older in the X1 homologous region which carries a huge inversion that occurred as early as 55–48 Ma, genetic degeneration of the neo-Y appears to be only moderate. Transcriptomic analysis showed that sex chromosomes harbor 87 genes, which may serve important functions in the testis. The accumulation of such male-beneficial genes, a large inversion on the X1 homologous region and fusion to X2 appear to be the main drivers of neo-Y evolution in the spotted knifejaw. The availability of high-quality assemblies of the neo-Y and both X chromosomes make this fish an ideal model for a better understanding of the variability of sex determination mechanisms and of sex chromosome evolution. KW - neo-Y KW - evolution; KW - spotted knifejaw KW - genome Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-364215 VL - 38 ER - TY - JOUR A1 - Letunic, Ivica A1 - Bork, Peer T1 - Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation JF - Nucleic Acids Research N2 - The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363803 VL - 49 ER -