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Along with barley and rice, maize provides staple food for more than half of the world population. Maize ears are regularly infected with fungal pathogens of the Fusarium genus, which, besides reducing yield, also taint grains with toxic metabolites. In an earlier work, we have shown that maize ears infection with single Fusarium strains was detectable through volatile sensing. In nature, infection most commonly occurs with more than a single fungal strain; hence we tested how the interactions of two strains would modulate volatile emission from infected ears. For this purpose, ears of a hybrid and a dwarf maize variety were simultaneously infected with different strains of Fusarium graminearum and F. verticillioides and, the resulting volatile profiles were compared to the ones of ears infected with single strains. Disease severity, fungal biomass, and the concentration of the oxylipin 9-hydroxy octadecadienoic acid, a signaling molecule involved in plant defense, were monitored and correlated to volatile profiles. Our results demonstrate that in simultaneous infections of hybrid and dwarf maize, the most competitive fungal strains had the largest influence on the volatile profile of infected ears. In both concurrent and single inoculations, volatile profiles reflected disease severity. Additionally, the data further indicate that dwarf maize and hybrid maize might emit common (i.e., sesquiterpenoids) and specific markers upon fungal infection. Overall this suggests that volatile profiles might be a good proxy for disease severity regardless of the fungal competition taking place in maize ears. With the appropriate sensitivity and reliability, volatile sensing thus appears as a promising tool for detecting fungal infection of maize ears under field conditions.
Circular RNAs (circRNAs), an important class of regulatory RNAs, have been shown to be the most prevalent in the brain compared with other tissues. However the processes governing their biogenesis in neurons are still elusive. Moreover, little is known about whether and how different biogenesis factors work in synchrony to generate neuronal circRNAs. To address this question, we pharmacologically inhibited the spliceosome and profiled rat neuronal circRNAs using RNA sequencing. We identified over 100 circRNAs that were up-regulated and a few circRNAs that were down-regulated upon spliceosome inhibition. Bioinformatic analysis revealed that up-regulated circRNAs possess significantly longer flanking introns compared with the un-changed circRNA population. Moreover, the flanking introns of up-regulated circRNAs harbor a higher number of distinct repeat sequences and more reverse complementary motifs compared with the unchanged circRNAs. Taken together, our data demonstrate that the biogenesis of circRNAs containing distinct intronic features becomes favored under conditions of limited spliceosome activity.
Cardiac trabeculation is one of the essential processes required for the formation of a competent ventricular wall, whereby clusters of ventricular cardiomyocytes (CMs) from a single layer delaminate and expand into the cardiac jelly to form sheet-like projections in the developing heart (Samsa et al., 2013). Several congenital heart diseases are associated with defects in the formation of these trabeculae and lead to embryonic lethality (Jenni et al., 1999; Zhang et al., 2013, Jenni et al., 2001; Towbin 2010). It has been experimentally shown that lack of Nrg1/ErbB2/ErbB4, Angipoetin1/Tie2, EphrinB2/B4, BMP10, or any component of the Notch signaling pathway can cause defective trabeculation. Moreover, changes in blood flow and/or contractility can also affect trabeculation (Samsa et al., 2013). Together, these observations demonstrate that cardiac trabeculation is a highly dynamic and regulated process.
Trabeculation is a morphogenetic process that requires control over cell shape changes and rearrangements, similar to those observed during EMT. Epithelial cells within an epithelium are polarized and establish cell-cell junctions with the neighboring cells (Ikenouchi et al., 2003; Ferrer-vaquer et al., 2010), thus epithelial cell polarity is an important feature to maintain cell shape and tissue structure. During developmental processes such as cell migration and cell division or in disease states epithelial polarity might be disrupted. As a consequence of this alteration, cells lose their tight cell-cell adhesions, undergo cytoskeletal rearrangements, change their shape and gain migratory properties becoming mesenchymal cells (Micalizzi et al., 2010). In epithelial cells, apicobasal polarity is regulated by a conserved set of core complexes, including the PAR, Scribble and Crumbs complexes (Kemphues et al., 1988; Bilder and Perrimon, 2000; Teppas et al., 1984). The polarity proteins composing these complexes interact in a well organized and coordinated-manner creating molecular asymmetry along the apicobasal axis of the cell. In turn, this crosstalk regulates the maturation and stabilization of the junctions between cells and cytoskeleton in order to strengthen cell polarization (Roignot et al., 2013). Amongst the different polarity complex, Crumbs has been shown to be a key regulator of apicobasal polarity during development in both vertebrates and invertebrates (Tepass et al., 1990; Fan et al., 2004).
Here, taking advantage of zebrafish as a model organism, I study in vivo at single cell resolution changes in CM apicobasal polarity during cardiac trabeculation. Moreover, I show which factors regulate CM apicobasal polarity during this process. In addition, I dissect the role of the polarity complex Crumbs in regulating CM junctional rearrangements and the formation of the trabecular network.
In the 'Golden Age of Antibiotics', between 1940 and 1970, the global pharmaceutical companies discovered many antibiotics, such as cephalosporins, tetracyclines, aminoglycosides, glycopeptides, etc., as well as antifungal and antiparisitic agents. Due to several reasons, e.g. the steady re-discovery of already known NPs and the associated high costs, many pharmaceutical companies have significantly scaled back or totally abandoned their NP discovery programs since the late 20th century. Instead those companies started to focus on drug discovery based on combinatorial synthesis and thereby on the creation of enormous synthetic libraries containing small molecules. Unfortunately, this synthetic approach dealing with the optimization of existing NP or antibiotic has its limitations. As a result, leading pharmaceutical companies are re-conducting NPs research to discover new antimicrobials for the upcoming antimicrobial resistance threat. The Natural Product Center of Excellence, a collaboration between Sanofi-Aventis and Fraunhofer IME, is advancing in this context the discovery and development of novel antimicrobial agents for the treatment of infectious diseases through the testing of Sanofi's microbial extract library and strain collection. The aim of the present PhD thesis was the discovery and isolation of novel antimicrobial compounds with improved activities and/or novel MOAs as potential lead compound for a further drug discovery.
The identification of heat stress (HS)-resilient germplasm is important to ensure food security under less favorable environmental conditions. For that, germplasm with an altered activity of factors regulating the HS response is an important genetic tool for crop improvement. Heat shock binding protein (HSBP) is one of the main negative regulators of HS response, acting as a repressor of the activity of HS transcription factors. We identified a TILLING allele of Solanum lycopersicum (tomato) HSBP1. We examined the effects of the mutation on the functionality of the protein in tomato protoplasts, and compared the thermotolerance capacity of lines carrying the wild-type and mutant alleles of HSBP1. The methionine-to-isoleucine mutation in the central heptad repeats of HSBP1 leads to a partial loss of protein function, thereby reducing the inhibitory effect on Hsf activity. Mutant seedlings show enhanced basal thermotolerance, while mature plants exhibit increased resilience in repeated HS treatments, as shown by several physiological parameters. Importantly, plants that are homozygous for the wild-type or mutant HSBP1 alleles showed no significant differences under non-stressed conditions. Altogether, these results indicate that the identified mutant HSBP1 allele can be used as a genetic tool in breeding, aiming to improve the thermotolerance of tomato varieties.
Truffle fungi are well known for their enticing aromas partially emitted by microbes colonizing truffle fruiting bodies. The identity and diversity of these microbes remain poorly investigated, because few studies have determined truffle-associated bacterial communities while considering only a small number of fruiting bodies. Hence, the factors driving the assembly of truffle microbiomes are yet to be elucidated. Here we investigated the bacterial community structure of more than 50 fruiting bodies of the black truffle Tuber aestivum in one French and one Swiss orchard using 16S rRNA gene amplicon high-throughput sequencing. Bacterial communities from truffles collected in both orchards shared their main dominant taxa: while 60% of fruiting bodies were dominated by α-Proteobacteria, in some cases the β-Proteobacteria or the Sphingobacteriia classes were the most abundant, suggesting that specific factors (i.e., truffle maturation and soil properties) shape differently truffle-associated microbiomes. We further attempted to assess the influence in truffle microbiome variation of factors related to collection season, truffle mating type, degree of maturation, and location within the truffle orchards. These factors had differential effects between the two truffle orchards, with season being the strongest predictor of community variation in the French orchard, and spatial location in the Swiss one. Surprisingly, genotype and fruiting body maturation did not have a significant effect on microbial community composition. In summary, our results show, regardless of the geographical location considered, the existence of heterogeneous bacterial communities within T. aestivum fruiting bodies that are dominated by three bacterial classes. They also indicate that factors shaping microbial communities within truffle fruiting bodies differ across local conditions.
This review summarizes studies of protection against singlet oxygen and radical damage by carotenoids. The main focus is on how substitutions of the carotenoid molecules determine high antioxidant activities such as singlet oxygen quenching and radical scavenging. Applied assays were carried out either in vitro in solvents or with liposomes, and in a few cases with living organisms. In the latter, protection by carotenoids especially of photosynthesis against light- and UV-stress is of major importance, but also heterotrophic organisms suffer from high light and UV exposure which can be alleviated by carotenoids. Carotenoids to be compared include C30, C40 and C50 molecules either acyclic, monocyclic or bicyclic with different substitutions including sugar and fatty acid moieties. Although some studies are difficult to compare, there is a tendency towards mono and bicyclic carotenoids with keto groups at C-4/C-4’ and the longest possible polyene structure functions to act best in singlet oxygen quenching and radical scavenging. Size of the carotenoid and lipophilic substituents such as fatty acids seem to be of minor importance for their activity but hydroxyl groups at an acyclic end and especially glycosylation of these hydroxyl groups enhance carotenoid activity.
Hereditary Parkinson’s disease (PD) can be triggered by an autosomal dominant overdose of alpha-Synuclein (SNCA) as stressor or the autosomal recessive deficiency of PINK1 Serine/Threonine-phosphorylation activity as stress-response. We demonstrated the combination of PINK1-knockout with overexpression of SNCAA53T in double mutant (DM) mice to exacerbate locomotor deficits and to reduce lifespan. To survey posttranslational modifications of proteins underlying the pathology, brain hemispheres of old DM mice underwent quantitative label-free global proteomic mass spectrometry, focused on Ser/Thr-phosphorylations. As an exceptionally strong effect, we detected >300-fold reductions of phosphoThr1928 in MAP1B, a microtubule-associated protein, and a similar reduction of phosphoSer3781 in ANK2, an interactor of microtubules. MAP1B depletion is known to trigger perturbations of microtubular mitochondria trafficking, neurite extension, and synaptic function, so it was noteworthy that relevantly decreased phosphorylation was also detected for other microtubule and microfilament factors, namely MAP2S1801, MARK1S394, MAP1AT1794, KIF1AS1537, 4.1NS541, 4.1GS86, and ADD2S528. While the MAP1B heavy chain supports regeneration and growth cones, its light chain assists DAPK1-mediated autophagy. Interestingly, relevant phosphorylation decreases of DAPK2S299, VPS13DS2429, and VPS13CS2480 in the DM brain affected regulators of autophagy, which are implicated in PD. Overall, significant downregulations were enriched for PFAM C2 domains, other kinases, and synaptic transmission factors upon automated bioinformatics, while upregulations were not enriched for selective motifs or pathways. Validation experiments confirmed the change of LC3 processing as reflection of excessive autophagy in DM brain, and dependence of ANK2/MAP1B expression on PINK1 levels. Our new data provide independent confirmation in a mouse model with combined PARK1/PARK4/PARK6 pathology that MAP1B/ANK2 phosphorylation events are implicated in Parkinsonian neurodegeneration. These findings expand on previous observations in Drosophila melanogaster that the MAP1B ortholog futsch in the presynapse is a primary target of the PARK8 protein LRRK2, and on a report that MAP1B is a component of the pathological Lewy body aggregates in PD patient brains. Similarly, ANK2 gene locus variants are associated with the risk of PD, ANK2 interacts with PINK1/Parkin-target proteins such as MIRO1 or ATP1A2, and ANK2-derived peptides are potent inhibitors of autophagy.
Transposable elements (TEs) are replicating genetic elementst hat comprise up to 50% of mammalian genomes. A specific class of TEs are retrotransposons that proliferate by transcription into a RNA intermediate, followed by genomic reintegration into another locus (so called “copy & paste” mechanism). Due to the lack of removal mechanisms and very rare parallel insertions, the presence of TE insertions at ortholgous genomic loci in multiple taxa provides a virtually homoplasy free phylogenetic marker. So far, developing phylogenetically informative markers from TE insertions has been a tedious work of testing hundreds of putative candidate loci in a trial-and error approach with low success rate. Hence, phylogenetic studies using TE insertions were often limited to a few dozen markers.
Recently, genome sequencing of multiple species using reference-mapping allowed the identification of genome-scale datasets of TE insertions. and made the ad-hoc development of phylogenetic informative markers possible. However, genome scale TE detection methods have rarely been applied to non model organisms in which data availability and quality is comparably limited. In this thesis, I developed the TeddyPi pipeline (TE detection and discovery for phylogenetic inference), a software tool that made it possible to obtain reliable genome-scale TE insertion data from low-coverage genomes. This was achieved by integrating the data from multiple TE and structural variation callers as well as applying a stringent filtering pipeline to exclude low-quality insertion calls. Whole-genome sequencing datasets of bears (Ursidae) and baleen whales (Mysticeti) were used to apply TE based phylogenetic inference and evaluate the method in comparison to sequence-based phylogenomic analyses.
In the bear genomes, TeddyPi identified 150,513 high-quality transposable element (TE) insertions, which allowed me to reconstruct the evolutionary history of bears despite extensive phylogenetic conflict (Lammers et al., 2017). The large number of detected TE insertions made also detailed network analyses possible that visualize the phylogenetic conflict. Experimental polymerase chain reaction (PCR) assays validated up to 93 % of the computationally identified TE loci and demonstrated the high accuracy of the dataset underlying the phylogenetic analyses.
Second, I present the initial genome sequencing of six baleen whales and a detailed investigation of their evolutionary history using TE insertions and established sequence-based phylogenomic methods. The taxon sampling of baleen whales included iconic species like the blue whale (Balaneoptera musculus) or the humpback whale (Megaptera novaengliae) (Árnason et al., 2018). A sequence-based reconstruction of the baleen whale species tree solved the long-debated phylogenetic position of the gray whale (Echrichtius robustus) within rorquals (Balaneopteridae) for the first time with high statistical support. Furthermore, the genome data made it possible to identify large extent of phylogenetic conflict for divergences during the radiation of rorquals that occurred 7-10 million years ago (Ma).
The phylogenomic analyses of 91,589 TE insertions in the whale genomes confirmed the sequence-based topology (Lammers et al., 2019). The quantification of phylogenetic signals obtained from the TE insertions revealed a high degree of discordance for the divergence of the gray whale and rorquals. Despite the large genome-scale dataset, statistical tests showed only marginal support for a bifurcating divergence of gray whales and the rorqual species. The limited statistical support for a strictly bifurcating tree obtained from genome-scale datasets of thousands of markers demonstrates the importance for including phylogenetic networks for displaying evolutionary divergences.
In conclusion, this thesis shows that identification of TE insertions from whole-genome resequencing provides plentiful and accurate phylogenomic markers. For the application in non model organisms, I provide a easy-to-use software to integrate multiple datasets from TE and structural variation callers in order to obtain reliable and ascertainment-bias free datasets. Detecting genome-scale datasets of TE insertions in two case studies demonstrates the applicability of this marker system for phylogenetic reconstruction and inferring phylogenetic conflict.
The haloarchaeon Haloferax volcanii contains nearly 2800 small non-coding RNAs (sRNAs). One intergenic sRNA, sRNA132, was chosen for a detailed characterization. A deletion mutant had a growth defect and thus underscored the importance of sRNA132. A microarray analysis identified the transcript of an operon for a phosphate-specific ABC transporter as a putative target of sRNA132. Both the sRNA132 and the operon transcript accumulated under low phosphate concentrations, indicating a positive regulatory role of sRNA132. A kinetic analysis revealed that sRNA132 is essential shortly after the onset of phosphate starvation, while other regulatory processes take over after several hours. Comparison of the transcriptomes of wild-type and the sRNA132 gene deletion mutant 30 min after the onset of phosphate starvation revealed that sRNA132 controls a regulon of about 40 genes. Remarkably, the regulon included a second operon for a phosphate-specific ABC transporter, which also depended on sRNA132 for rapid induction in the absence of phosphate. Competitive growth experiments of the wild-type and ABC transporter operon deletion mutants underscored the importance of both transporters for growth at low phosphate concentrations. Northern blot analyses of four additional members of the sRNA132 regulon verified that all four transcripts depended on sRNA132 for rapid regulation after the onset of phosphate starvation. Importantly, this is the first example for the transient importance of a sRNA for any archaeal and bacterial species. In addition, this study unraveled the first sRNA regulon for haloarchaea.
As a flavor and platform chemical, m-cresol (3-methylphenol) is a valuable industrial compound that currently is mainly synthesized by chemical methods from fossil resources. In this study, we present the first biotechnological de novo production of m-cresol from sugar in complex yeast extract-peptone medium with the yeast Saccharomyces cerevisiae. A heterologous pathway based on the decarboxylation of the polyketide 6-methylsalicylic acid (6-MSA) was introduced into a CEN.PK yeast strain. For synthesis of 6-MSA, expression of different variants of 6-MSA synthases (MSASs) were compared. Overexpression of codon-optimized MSAS from Penicillium patulum together with activating phosphopantetheinyl transferase npgA from Aspergillus nidulans resulted in up to 367 mg/L 6-MSA production. Additional genomic integration of the genes had a strongly promoting effect and 6-MSA titers reached more than 2 g/L. Simultaneous expression of 6-MSA decarboxylase patG from A. clavatus led to the complete conversion of 6-MSA and production of up to 589 mg/L m-cresol. As addition of 450–750 mg/L m-cresol to yeast cultures nearly completely inhibited growth our data suggest that the toxicity of m-cresol might be the limiting factor for higher production titers.
Mapping biodiversity is the marathon of the 21st Century as an answer to the present extinction crisis. A century in which science is also characterised by large scientific datasets collected through new technologies aiming to fill gaps in our knowledge of species distributions. However, most species records rely on observations that are not linked to specimens, which does not allow verification of species hypotheses by other scientists. Natural history museums form a verifiable source of biodiversity records which were made by taxonomists. Nonetheless, these museums seem to be forgotten by biologists in scientific fields other than taxonomy or systematics. Naturalis Biodiversity Center (NBC) in Leiden is care keeper of large collections of marine organisms, which were sampled in the Northeast Atlantic during the CANCAP and Tyro Mauritania II expeditions (1976–1988). Many octocorals were sampled and deposited in the NBC collection, where they became available for study and were partially identified by the senior author (M.G.) in the 1980s. Nonetheless, no checklist or taxonomic revision was published so far with the complete results. In 2016 the first author visited NBC to examine NE Atlantic Plexauridae octocorals. Plexauridae octocoral-vouchered records were listed and mapped to reveal high standard primary biodiversity records unreported so far for the NE Atlantic Ocean. Twenty-four Plexauridae species with ~ six putative new species to science were discovered and eleven new biogeographical records were made from distinct Macaronesian archipelagos. Finally, new depth range records were found for three species at sea basin level and for eight species at a regional scale.
In homeostatic scaling at central synapses, the depth and breadth of cellular mechanisms that detect the offset from the set-point, detect the duration of the offset and implement a cellular response are not well understood. To understand the time-dependent scaling dynamics we treated cultured rat hippocampal cells with either TTX or bicucculline for 2 hr to induce the process of up- or down-scaling, respectively. During the activity manipulation we metabolically labeled newly synthesized proteins using BONCAT. We identified 168 newly synthesized proteins that exhibited significant changes in expression. To obtain a temporal trajectory of the response, we compared the proteins synthesized within 2 hr or 24 hr of the activity manipulation. Surprisingly, there was little overlap in the significantly regulated newly synthesized proteins identified in the early- and integrated late response datasets. There was, however, overlap in the functional categories that are modulated early and late. These data indicate that within protein function groups, different proteomic choices can be made to effect early and late homeostatic responses that detect the duration and polarity of the activity manipulation.
The nuclear exosome and its essential co-factor, the RNA helicase MTR4, play crucial roles in several RNA degradation pathways. Besides unwinding RNA substrates for exosome-mediated degradation, MTR4 associates with RNA-binding proteins that function as adaptors in different RNA processing and decay pathways. Here, we identify and characterize the interactions of human MTR4 with a ribosome processing adaptor, NVL, and with ZCCHC8, an adaptor involved in the decay of small nuclear RNAs. We show that the unstructured regions of NVL and ZCCHC8 contain short linear motifs that bind the MTR4 arch domain in a mutually exclusive manner. These short sequences diverged from the arch-interacting motif (AIM) of yeast rRNA processing factors. Our results suggest that nuclear exosome adaptors have evolved canonical and non-canonical AIM sequences to target human MTR4 and demonstrate the versatility and specificity with which the MTR4 arch domain can recruit a repertoire of different RNA-binding proteins.
Nanoplastics (NP) and microplastics (MP) accumulate in our environment as a consequence of the massive consumption of plastics. Huge knowledge-gaps exist regarding uptake and fate of plastic particles in micro- and nano-dimensions in humans as well as on their impact on human health.
This study investigated the transport and effects of 50 nm and 0.5 μm COOH-modified polystyrene (PS) particles, as representatives for NP and MP, in different biological models in vitro. Acute toxicity and potential translocation of the particles were studied at the human intestinal and placental barrier using advanced in vitro co-culture models. Furthermore, embryotoxicity and genotoxicity were investigated as highly sensitive endpoints.
Polystyrene was not acutely toxic in both sizes (nano- and microparticles). No transport across the intestinal and placental barrier but a cellular uptake and intracellular accumulation of PS nano- and microparticles were determined. The particles were identified as weak embryotoxic and non-genotoxic.
In contrast to single-organ studies, this multi-endpoint study is providing a data-set with the exact same type of particles to compare organ-specific outcomes. Our study clearly shows the need to investigate other types of plastics as well as towards long-term or chronic effects of plastic particles in different biological models in vitro.
The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage was unclear. Here we report that, as of March 2017, Sci-Hub’s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.2% of articles published in toll access journals. We find that coverage varies by discipline and publisher and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, green open access via licit services is quite limited, while Sci-Hub provides greater coverage than a major research university. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model will become unsustainable.
The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent of Sci-Hub's coverage was unclear. As of March 2017, we find that Sci-Hub's database contains 68.9% of all 81.6 million scholarly articles, which rises to 85.2% for those published in closed access journals. Furthermore, Sci-Hub contains 77.0% of the 5.2 million articles published by inactive journals. Coverage varies by discipline, with 92.8% coverage of articles in chemistry journals compared to 76.3% for computer science. Coverage also varies by publisher, with the coverage of the largest publisher, Elsevier, at 97.3%. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. Finally, we estimate that over a six-month period in 2015–2016, Sci-Hub provided access for 99.3% of valid incoming requests. Hence, the scope of this resource suggests the subscription publishing model is becoming unsustainable. For the first time, the overwhelming majority of scholarly literature is available gratis to anyone with an Internet connection.
The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage has been unclear. Here we report that, as of March 2017, Sci-Hub’s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable.
As adapter molecules to convert the nucleic acid information into the amino acid sequence, tRNAs play a central role in protein synthesis. To fulfill this function in a reliable way, tRNAs exhibit highly conserved structural features common in all organisms and in all cellular compartments active in translation. However, in mitochondria of metazoans, certain dramatic deviations from the consensus tRNA structure are described, where some tRNAs lack the D- or T-arm without losing their function. In Enoplea, this miniaturization comes to an extreme, and functional mitochondrial tRNAs can lack both arms, leading to a considerable size reduction. Here, we investigate the secondary and tertiary structure of two such armless tRNAs from Romanomermis culicivorax. Despite their high AU content, the transcripts fold into a single and surprisingly stable hairpin structure, deviating from standard tRNAs. The three-dimensional form is boomerang-like and diverges from the standard L-shape. These results indicate that such unconventional miniaturized tRNAs can still fold into a tRNA-like shape, although their length and secondary structure are very unusual. They highlight the remarkable flexibility of the protein synthesis apparatus and suggest that the translational machinery of Enoplea mitochondria may show compensatory adaptations to accommodate these armless tRNAs for efficient translation.
Der DNA-Translokator von T. thermophilus HB27, ebenso wie Typ-IV-Pili (T4P), sind Multiproteinkomplexe, die die Membranen und das Periplasma durchspannen. Sie sind ähnlich aufgebaut und enthalten identische Proteine. Der DNA-Translokator vermittelt Transport von DNA in das Zellinnere während der natürlichen Transformation. T4P sind filamentöse Zellorganellen, die an der inneren Membran assembliert werden und bis zu mehrere Mikrometer aus der Zelle hinausragen. Sie dienen der Anhaftung und Fortbewegung der Zellen auf Oberflächen.
Das Ziel dieser Arbeit war es, die Funktionen einzelner Komponenten der Komplexe und ihrer Proteindomänen bei der natürlichen Transformation, der T4P-Assemblierung und den durch T4P vermittelten Funktionen Adhäsion und „twitching motility“ aufzuklären.
Es sind neun Proteine bekannt, die eine duale Rolle als Komponenten des DNA-Translokators und des T4P spielen. Eines dieser Proteine ist die Assemblierungs-ATPase PilF, die Hexamere bildet. Diese cytoplasmatischen ATPase-Komplexe stellen die Energie für die Assemblierung der T4P bereit, ebenso wie für die Aufnahme freier DNA. Es ist jedoch bisher nicht geklärt, wie die durch PilF bereitgestellte Energie auf die anderen Komponenten des DNA-Translokators/T4P übertragen wird.
In dieser Arbeit konnte gezeigt werden, dass PilF an das cytoplasmatische Protein PilM des T4P und DNA-Translokators bindet. Zudem konnten Proteinkomplexe bestehend aus den Proteinen PilM, PilN und PilO heterolog produziert und aus Zellmembranen koisoliert werden. PilF interagierte mit diesen PilMNO-Komplexen via PilM. Diese Interaktionen führt zur Stimulierung der ATPase-Aktivität von PilF. Dies deutet an, dass PilM ein Kupplungsprotein ist, welches die Assemblierungs-ATPase PilF physisch und funktionell mit dem T4P/DNA-Translokator über den PilMNO-Komplex verbindet.
Neben PilF standen Präpiline von T. thermophilus im Fokus dieser Arbeit. Präpiline sind Vorläuferproteine, die zu Pilinen prozessiert werden und als solche dann die Untereinheiten der Pilus-Strukturen bilden.
Zusammenfassend konnten die Rollen einzelner Präpilin-ähnlicher Proteine bei T4P-assoziierten Funktionen geklärt werden und es konnten erste Analysen zur Charakterisierung des weitestgehend unbekannten Proteins ComZ durchgeführt werden. Desweiteren liefert diese Arbeit Hinweise darauf, dass die membranassoziierten Proteine PilM, PilN und PilO Kupplungsproteine sind, die PilF mit den periplasmatischen Komponenten des T4P/DNA-Translokators verbinden und dadurch die ATPase-Aktivität von PilF stimulieren. Die Rollen einzelner Proteindomänen von PilF und PilM bei der Protein-Protein-Interaktion und der Bindung von Liganden wurden aufgeklärt, sowie ihre Funktionen bei den T4P-vermittelten Funktionen und der natürlichen Transformation.
Microenvironmental regulation of tumor progression and therapeutic response in brain metastasis
(2019)
Cellular and non-cellular components of the tumor microenvironment (TME) are emerging as key regulators of primary tumor progression, organ-specific metastasis, and therapeutic response. In the era of TME-targeted- and immunotherapies, cancer-associated inflammation has gained increasing attention. In this regard, the brain represents a unique and highly specialized organ. It has long been regarded as an immunological sanctuary site where the presence of the blood brain barrier (BBB) and blood cerebrospinal fluid barrier (BCB) restricts the entry of immune cells from the periphery. Consequently, tumor cells that metastasize to the brain were thought to be shielded from systemic immune surveillance and destruction. However, the detailed characterization of the immune landscape within border-associated areas of the central nervous system (CNS), such as the meninges and the choroid plexus, as well as the discovery of lymphatics and channels that connect the CNS with the periphery, have recently challenged the dogma of the immune privileged status of the brain. Moreover, the presence of brain metastases (BrM) disrupts the integrity of the BBB and BCB. Indeed, BrM induce the recruitment of different immune cells from the myeloid and lymphoid lineage to the CNS. Blood-borne immune cells together with brain-resident cell-types, such as astrocytes, microglia, and neurons, form a highly complex and dynamic TME that affects tumor cell survival and modulates the mode of immune responses that are elicited by brain metastatic tumor cells. In this review, we will summarize recent findings on heterotypic interactions within the brain metastatic TME and highlight specific functions of brain-resident and recruited cells at different rate-limiting steps of the metastatic cascade. Based on the insight from recent studies, we will discuss new opportunities and challenges for TME-targeted and immunotherapies for BrM.
The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop—a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect. We then use NMR spectroscopy to confirm the existence of this cation-binding site and to demonstrate its effects on RNA stability. Lastly, using quantum chemical calculations, we show that the cation-binding site is altering the electronic environment of the wild-type U-turn so that it is more similar to the cytosine mutant. The study reveals an amazingly complex and delicate interplay between various energy contributions shaping up the 3D structure and evolution of nucleic acids.
Autophagy, meaning “self-eating”, is an important cellular waste disposal mechanism. Thereby, damaged proteins, lipids and organelles are enclosed by autophagosomes and subsequently transported to the lysosomes for degradation into basic, cellular building blocks. Under basal conditions autophagy prevents the accumulation of defective and harmful material and generally promotes cell survival. However, several studies reported that hyperactivated autophagy, e.g. during developmental processes in lower eukaryotes, or during chemotherapeutic treatment of cancer cells, can also trigger cell death.
In recent years, autophagic cell death (ACD) has been considered as an alternative cell death pathway for tumor therapy, especially for solid tumors with high apoptosis resistance such as glioblastoma. Glioblastoma (GBM) is a very aggressive, malignant primary brain tumor with a median survival of ~ 15 months despite surgery and chemoradiotherapy. Accordingly, there is a great interest in improving GBM therapy through alternative cell death mechanisms. Interestingly, it has been shown that various substances, e.g. AT 101, cannabinoids and the combination of imipramine and ticlopidine (IM+TIC), induce ACD in GBM cells.
The aim of this project was to identify the underlying mechanisms of stress- and drug-induced ACD and its therapeutic potential for glioblastoma treatment. For detailed investigation of ACD, a CRISPR/Cas9-based approach was used to generate ATG5 and ATG7 knockouts as genetic models of autophagy deficiency. In a previous study of our lab it was demonstrated that administration of AT 101 triggers ACD in glioblastoma cells, which was associated with early mitochondrial fragmentation but no signs of apoptosis. Since mitochondrial fragmentation often precedes mitophagy, the first part of this thesis explored the potential role of mitophagy in AT 101-induced cell death.
ATG5-depleted cells confirmed that AT 101 induces ACD. In addition, treatment with AT 101 resulted in a pronounced mitochondrial depolarization, which was at least partly caused by the opening of the mitochondrial permeability pore. Global proteome analysis of AT 101-treated GBM cells revealed a robust decrease in mitochondrial protein clusters as well as a strong increase in the enzyme heme oxygenase-1 (HMOX1). Subsequent experiments for detailed investigation of mitophagy following AT 101 treatment (western blot, flow cytometric MTG and mt-mKeima, qRT-PCR of mitochondrial vs nuclear DNA) consistently indicated strong mitophagy induction by AT 101, which could be reduced by genetic or pharmacological inhibition of autophagy. Furthermore, siRNA-mediated knockdown experiments revealed that the selective mitophagy receptors BNIP3 and BNIP3L and the HMOX1 enzyme play an essential role in AT 101-induced mitophagy and subsequent cell death. Taken together, these data demonstrate that AT 101-induced mitochondrial dysfunction and HMOX1 induction synergize to promote excessive mitophagy with a lethal outcome in glioma cells.
The second part of this thesis focused on the identification of new substances that cause ACD and the investigation of the underlying cell death pathways. Using a cell death screen of the ENZO Screen-Well™ autophagy library in MZ-54 wild-type vs ATG5 and ATG7-depleted cells, loperamide, pimozide, and STF-62247 were identified as ACD-inducing agents. The increase of the autophagic flux and the induction of ACD by these substances was confirmed by using different ATG5 and ATG7 knockout cell lines and the already established positive control IM+TIC.
In contrast to AT 101, IM+TIC, STF-62247, loperamide and pimozide produced neither mitochondrial dysfunction nor mitophagy. Interestingly, it has been described that imipramine, loperamide and pimozide inhibit the lysosomal enzyme acid sphingomyelinase, which is associated with impaired lipid transport. Global proteome analysis and cholesterol staining confirmed that all four substances, but especially loperamide and pimozide, inhibit cellular lipid transport, leading to massive lipid accumulation in the lysosomes. In the further course of the experiments, the connection between defective lipid transport and autophagy was investigated in more detail. On the one hand, the defective lipid transport contributed to the induction of autophagy, on the other hand the massive accumulation of lipids led to lysosomal membrane damage, inhibition of lysosomal degradation at later time points and finally to a lysosomal cell death. Remarkably, it has been shown that hyperactivated autophagy by IM+TIC, loperamide and pimozide massively promotes lysosomal membrane damage. This result highlights the difficulties of a clear distinction between autophagic and lysosomal cell death.
In summary, two new signaling pathways that induce autophagic cell death in GBM cells and may be relevant for glioblastoma therapy were investigated in this study.
Altered microRNA (miRNA) expression is a hallmark of many cancer types. The combined analysis of miRNA and messenger RNA (mRNA) expression profiles is crucial to identifying links between deregulated miRNAs and oncogenic pathways. Therefore, we investigated the small non-coding (snc) transcriptomes of nine clear cell renal cell carcinomas (ccRCCs) and adjacent normal tissues for alterations in miRNA expression using a publicly available small RNA-Sequencing (sRNA-Seq) raw-dataset. We constructed a network of deregulated miRNAs and a set of differentially expressed genes publicly available from an independent study to in silico determine miRNAs that contribute to clear cell renal cell carcinogenesis. From a total of 1,672 sncRNAs, 61 were differentially expressed across all ccRCC tissue samples. Several with known implications in ccRCC development, like the upregulated miR-21-5p, miR-142-5p, as well as the downregulated miR-106a-5p, miR-135a-5p, or miR-206. Additionally, novel promising candidates like miR-3065, which i.a. targets NRP2 and FLT1, were detected in this study. Interaction network analysis revealed pivotal roles for miR-106a-5p, whose loss might contribute to the upregulation of 49 target mRNAs, miR-135a-5p (32 targets), miR-206 (28 targets), miR-363-3p (22 targets), and miR-216b (13 targets). Among these targets are the angiogenesis, metastasis, and motility promoting oncogenes c-MET, VEGFA, NRP2, and FLT1, the latter two coding for VEGFA receptors.
The lipidome of the marine hyperthermophilic archaeon Pyrococcus furiosus was studied by means of combined thin-layer chromatography and MALDI-TOF/MS analyses of the total lipid extract. 80–90% of the major polar lipids were represented by archaeol lipids (diethers) and the remaining part by caldarchaeol lipids (tetraethers). The direct analysis of lipids on chromatography plate showed the presence of the diphytanylglycerol analogues of phosphatidylinositol and phosphatidylglycerol, the N-acetylglucosamine-diphytanylglycerol phosphate plus some caldarchaeol lipids different from those previously described. In addition, evidence for the presence of the dimeric ether lipid cardiolipin is reported, suggesting that cardiolipins are ubiquitous in archaea.
A large number of staphylinid beetles are closely associated with ants and termites (for review see Wilson 1971, Kistner 1979). Those species living with ants are commonly called myremcophiles. At least a few (Atemeles, Lomechusa) have "broken" the communication code of their host species and are thereby able to become completely integrated in the social system of the ants (Hölldolber 1967, 1970, 1971). In an attempt to understand the evolutionary pathways of this highly specialized social parasitic behavior, we studied closely related staphylinid species that do not live within the ant society but instead occupy the foraging trails and garbage dumps of an ant nest. ...
Structured illumination microscopy (SIM) is part of the super-resolution methods developed at the beginning of this century. To produce a super-resolution image SIM requires three things: 1) illumination of the sample with a periodic pattern, 2) acquisition of multiple images per plane under different pattern’s phases and orientations and 3) the processing of these images has to be carried with a reconstruction algorithm. The result of the reconstruction is an image with a resolution gain that is proportional to the frequency of the pattern (po). The typical SIM set-up uses an epi-fluorescence configuration, thus the interference angle of the beams that create the pattern is restricted by the angular aperture of the objective. Under this restriction the maximum value of po is given by the cut-off frequency of the objective lens and sets at 2 the maximum resolution gain of SIM under linear illumination.
In the first part of this thesis we present the implementation and characterization of the 2D-SIM set-up designed by Dr. Bo-Jui Chang (B-J. Chang et al., PNAS 2017), this design exploits the concept introduced by light-sheet microscopy, i.e. separation of illumination and detection paths to obtain resolution gains larger than the usual two-fold (Chapter 3). The set-up is named coherent structured illumination light-sheet based fluorescence microscopy (csiLSFM) and it consists of a triangular array of three objectives, such that two are used for illumination and one for detection. With the independent illumination arms is possible to interfere two coherent light-sheets at angles beyond the angular aperture of the detection lens, attaining the maximum interference angle of 180° when the light-sheets counter-propagate. This condition delivers a pattern with a po 1.4 times larger than the cut-off frequency (ωo), hence our set-up provides generic resolution gains of 2.4.
The extraction of the high spatial frequencies that produce the resolution gain in the csiLSFM is a challenge due to a low pattern modulation. The low modulation inherently arises because the frequency associated to the pattern period lies beyond the cut-off frequency of the detection lens. To overcome this challenge we developed a filtering strategy that facilitates the withdrawal of information from a SIM data set, simultaneously the proposed filtering process optimizes the reconstruction algorithm by reducing the periodic artifacts that are recurrent in SIM images. In this same chapter we also performed an spectral analysis of the artifacts and determined that they originate from irregularities in the power spectrum that occur due to the partial or total lack of certain spatial frequencies (fig.4.2 and 4.3), our reconstruction reduces this information drops and diminishes the artifact occurrence. The relevance of our reconstruction pipeline is that it delivers a standardized process to enhance the SIM image in a current context in which the commonly used reconstruction algorithms employ empirical tuning to improve it (fig.4.13). Moreover, the pipeline is applicable to the csiLSFM data and also to images acquired with any other 2D-/3D-SIM set-up (fig.4.10 and 4.11).
The processing of various image data sets acquired with the csiLSFM exposed us to the question of how low the modulation of the illumination pattern can be before no super-resolution frequencies can be extracted. Answering this question is important to guarantee that the SIM data contains enough spatial frequencies to provide significant resolution gains. Thus in chapter 5 we developed a quantitative metric to indirectly determine the pattern modulation from the SIM data and find its critical value to use it as evaluation criterion. We called this metric the quality factor (Q-factor) and it represents the normalized strength (amplitude) of the extracted frequencies respect to the Gaussian noise contained in the images. Through simulations we estimated that Q=0.11 is a critical value and a SIM data set requires this as minimum value is to deliver a significant resolution gain. Q works then as an assessment tool for classifying SIM data as optimal or sub-optimal, i.e. Q≥0.11 or Q<0.11. We demonstrated such application with data acquired in various SIM commercial set-ups to prove its feasibility in the field (fig.5.6-5.11)
As mentioned at the beginning of this abstract SIM requires a specialized set-up and a processing algorithm to produce super-resolution images. This thesis contributes to these two areas in the following aspects: first, in its linear version a structured illumination microscope is highly associated to a 2-fold resolution gain. Here we demonstrated the possibility of extending this gain to 2.4 using our custom set-up the csiLSFM. Second, a reconstructed SIM image is prone to artifacts due to the mathematical process it undergoes, here we analyzed the artifact sources and identified them with drops of spatial information in the reconstructed spectrum, based on these conclusions we designed a processing pipeline to facilitate the extraction of spatial frequencies and directly reduce artifacts. A third and final outcome of this thesis is the development and practical implementation of a quantitative index to evaluate the quality of SIM data in terms of its relevant information content (Q-factor). Accordingly, the overall contributions of this work were done in the areas of SIM set-up, SIM reconstruction procedure and SIM data evaluation.
Background: Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily.
Results: Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic.
Conclusions: The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
Unique features of a global human ectoparasite identified through sequencing of the bed bug genome
(2016)
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
Members of the Sm protein family are important for the cellular RNA metabolism in all three domains of life. The family includes archaeal and eukaryotic Lsm proteins, eukaryotic Sm proteins and archaeal and bacterial Hfq proteins. While several studies concerning the bacterial and eukaryotic family members have been published, little is known about the archaeal Lsm proteins. Although structures for several archaeal Lsm proteins have been solved already more than ten years ago, we still do not know much about their biological function, however one can confidently propose that the archaeal Lsm proteins will also be involved in RNA metabolism. Therefore, we investigated this protein in the halophilic archaeon Haloferax volcanii. The Haloferax genome encodes a single Lsm protein, the lsm gene overlaps and is co-transcribed with the gene for the ribosomal L37.eR protein. Here, we show that the reading frame of the lsm gene contains a promoter which regulates expression of the overlapping rpl37R gene. This rpl37R specific promoter ensures high expression of the rpl37R gene in exponential growth phase. To investigate the biological function of the Lsm protein we generated a lsm deletion mutant that had the coding sequence for the Sm1 motif removed but still contained the internal promoter for the downstream rpl37R gene. The transcriptome of this deletion mutant was compared to the wild type transcriptome, revealing that several genes are down-regulated and many genes are up-regulated in the deletion strain. Northern blot analyses confirmed down-regulation of two genes. In addition, the deletion strain showed a gain of function in swarming, in congruence with the up-regulation of transcripts encoding proteins required for motility.
Zinc finger domains are highly structured and can mediate interactions to DNA, RNA, proteins, lipids, and small molecules. Accordingly, zinc finger proteins are very versatile and involved in many biological functions. Eukaryotes contain a wealth of zinc finger proteins, but zinc finger proteins have also been found in archaea and bacteria. Large zinc finger proteins have been well studied, however, in stark contrast, single domain zinc finger µ-proteins of less than 70 amino acids have not been studied at all, with one single exception. Therefore, 16 zinc finger µ-proteins of the haloarchaeon Haloferax volcanii were chosen and in frame deletion mutants of the cognate genes were generated. The phenotypes of mutants and wild-type were compared under eight different conditions, which were chosen to represent various pathways and involve many genes. None of the mutants differed from the wild-type under optimal or near-optimal conditions. However, 12 of the 16 mutants exhibited a phenotypic difference under at least one of the four following conditions: Growth in synthetic medium with glycerol, growth in the presence of bile acids, biofilm formation, and swarming. In total, 16 loss of function and 11 gain of function phenotypes were observed. Five mutants indicated counter-regulation of a sessile versus a motile life style in H. volcanii. In conclusion, the generation and analysis of a set of deletion mutants demonstrated the high importance of zinc finger µ-proteins for various biological functions, and it will be the basis for future mechanistic insight.
Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.
BACKGROUND: Attention-Deficit/Hyperactivity Disorder (ADHD) is one of the most common neurodevelopmental disorders worldwide. As described in the DSM-5, ADHD is clinically heterogeneous with three main subtypes; predominant hyperactive, predominant attention deficit and combined. The severity of symptoms widely differs among the patients and interferes with the person functioning, negatively impacting social and occupational activities (American Psychiatric Association, 2013). Despite the many efforts, the etiology of the disorder is still unclear. Therefore, there is an increasing demand of models that would help elucidating the causative mechanisms of the disorder and, in parallel, would be valuable tools to discover new and effective treatments. The main goal of the study is the identification of disease specific cellular phenotypes related to Attention-Deficit/Hyperactivity Disorder (ADHD) in cellular models from patients carrying rare copy number variants (CNVs) in the PARK2 locus that have been previously associated with ADHD (Elia et al., 2010; Jarick et al., 2014).
METHODS: Human dermal fibroblast (HDF) cultures were obtained from skin punches and reprogrammed into human induced pluripotent stem cells (HiPSC) and successively induced to differentiate into HiPSC-derived dopaminergic neurons. Both HiPSC and HiPSC-derived neurons, were proven to be bona fide models by morphological analysis, RT-PCR, RT-qPCR, immunofluorescence, embryoid body assay, molecular karyotyping and dopamine level quantification. A total of six donors were selected for HiPSC and dopaminergic neuron generation: 3 adult ADHD PARK2 CNV risk carriers (1 duplication and 2 deletion carriers, 1 ADHD non-risk CNV variant carrier and 2 healthy controls).
We conducted stress-response experiments (nutrient deprivation and CCCP administration) that are well known to increase PARK2 expression, on both fibroblasts and HiPSC. After assessing PARK2 gene and protein expression levels, we evaluated the gene expression of genes that are involved with different processes orchestrated by PARK2. We then performed a series of assays with a special focus on mitochondrial function and energy metabolism (ATP production, basal oxygen consumption rates, ROS abundance) and evaluated changing in the mitochondrial network morphology.
To evaluate the effect of nicotine exposure, one of the best replicated prenatal risk factors for having a child later on diagnosed with ADHD, we treated HiPSC-derived dopaminergic neurons with smoking-relevant nicotine concentrations and evaluated PARK2 protein expression after treatment and gene expression by RNA sequencing.
RESULTS: The cell models created in this study passed all the characterization tests required to assess whether the lines can be considered bona fide models without underling genotype differences. The evaluation of patho-phenotypes connected with ADHD/PARK2 CNVs in HDF and HIPSC showed that, although PARK2 gene expression was unchanged, ADHD/PARK2 CNV carriers show different PARK2 protein levels possibly implying the presence of different post-transcriptional processes. ADHD/PARK2 CNV carriers show lower levels of ATP production and basal oxygen consumption rates compared to controls, a result in line with what was already reported in ADHD cybrids cells model (Verma et al., 2016). Our experiments indicate that both the amount of reactive oxygen species (ROS) and the mitochondrial network morphology is influenced by the treatment but not by the genotype. The evaluation of nicotine effects on HiPSC-derived dopaminergic neuron from aADHD patients showed no effects on PARK2 protein levels and gene expression. ADHD/PARK2 CNVs carriers show gene ontology enrichment in modules connected with the regulation of cell growth after nicotine acute treatment. Additionally, genes connected with energy production & oxidative stress response and extracellular matrix & cell adhesion were significantly differentially expressed after nicotine treatments.
CONCLUSIONS: This study points out the presence of impairment of mitochondrial energetics in cellular models derived from adult ADHD patients carrying rare CNVs within the PARK2 locus. In the last years, several studies have linked mitochondrial impairments to the etiology of psychiatric and neurodevelopmental disorders (McCann & Ross, 2018) and reported an overall increase of oxidative stress or insufficient response to oxidative damage both in children and adults with ADHD (Joseph, Zhang-James, Perl, & Faraone, 2015; Lopresti, 2015). Additionally, different groups have underlined an abnormal brain connectivity in ADHD patients in their work (Gehricke et al., 2017). Our preliminary investigation of the effects of a well-known prenatal risk factor for ADHD, nicotine gestation exposure, point out a susceptibility of the PARK2 CNVs carriers in processes involved in regulation of cell growth and in proteins connected with extracellular matrix composition and cell-adhesion molecules, all factors necessary for neuronal maturation and formation of proper neural connections (Washbourne et al., 2004). In conclusion, this study presents novel and fully validated cellular model systems to study the etiopathogenesis of ADHD based on rare CNVs in the PARK2 locus. Moreover, the identification of disease-relevant phenotypes in the model might be helpful in the future for testing new alternative medications.
Drebrin (DBN) regulates cytoskeletal functions during neuronal development, and is thought to contribute to structural and functional synaptic changes associated with aging and Alzheimer’s disease. Here we show that DBN coordinates stress signalling with cytoskeletal dynamics, via a mechanism involving kinase ataxia-telangiectasia mutated (ATM). An excess of reactive oxygen species (ROS) stimulates ATM-dependent phosphorylation of DBN at serine-647, which enhances protein stability and accounts for improved stress resilience in dendritic spines. We generated a humanized DBN Caenorhabditis elegans model and show that a phospho-DBN mutant disrupts the protective ATM effect on lifespan under sustained oxidative stress. Our data indicate a master regulatory function of ATM-DBN in integrating cytosolic stress-induced signalling with the dynamics of actin remodelling to provide protection from synapse dysfunction and ROS-triggered reduced lifespan. They further suggest that DBN protein abundance governs actin filament stability to contribute to the consequences of oxidative stress in physiological and pathological conditions.
Die Analyse von DNA-Sequenzen steht spätestens seit der Feststellung ihrer tragenden Rolle in der Vererbung organismischer Eigenschaften im Fokus biologischer Fragestellungen. Seit Kurzem wird mit modernsten Methoden die Untersuchung von kompletten Genomen ermöglicht. Dies eröffnet den Zugang zu genomweiten Informationen gegenüber begrenzt aussagekräftigen markerbasierten Analysen. Eine Genomsequenz ist die ultimative Quelle an organismischer Information. Allerdings sind diese Informationen oft aufgrund technischer und biologischer Gründe komplex und werfen meist mehr Fragen auf, als sie beantworten.
Die Rekonstruktion einer bislang unbekannten Genomsequenz aus kurzen Sequenzen stellt eine technische Herausforderung dar, die mit grundlegenden, aber in der Realität nicht zwingend zutreffenden Annahmen verbunden ist. Außerdem können biologische Faktoren, wie Repeatgehalt oder Heterozygotie, die Fehlerrate einer Assemblierung stark beeinflussen. Die Beurteilung der Qualität einer de novo Assemblierung ist herausfordernd, aber zugleich äußerst notwendig. Anschließend ist eine strukturelle und funktionale Annotation von Genen, kodierenden Bereichen und repeats nötig, um umfangreiche biologische Fragestellungen beantworten zu können. Ein qualitativ hochwertiges und annotiertes assembly ermöglicht genomweite Analysen von Individuen und Populationen. Diese Arbeit beinhaltet die Assemblierung und Annotation des Genoms der Süßwasserschnecke Radix auricularia und eine Studie vergleichender Genomik von fünf Individuen aus verschiedenen molekularen Gruppen (MOTUs).
Mollusken beherbergen nach den Insekten die größte Artenvielfalt innerhalb der Tierstämme und besiedeln verschiedenste, teils extreme, Habitate. Trotz der großen Bedeutung für die Biodiversitätsforschung sind verhältnismäßig wenige genomische Daten öffentlich verfügbar. Zudem sind Arten der Gattung Radix auch aufgrund ihrer großen geografischen Verbreitung in diversen biologischen Disziplinen als Modellorganismen etabliert. Eine annotierte Genomsequenz ermöglicht über bereits untersuchte Felder hinaus die Forschung an grundlegenden biologischen Fragestellungen, wie z.B. die Funktionsweise von Hybridisierung und Artbildung. Durch Assemblierung und scaffolding von sechs whole genome shotgun Bibliotheken verschiedener insert sizes und einem transkriptbasiertem scaffolding konnte trotz des hohen Repeatgehalts ein vergleichsweise kontinuierliches assembly erhalten werden. Die erhebliche Differenz zwischen der Gesamtlänge der Assemblierung und der geschätzten Genomgröße konnte zum Großteil auf kollabierte repeats zurückgeführt werden.
Die strukturelle Annotation basierend auf Transkriptomen, Proteinen einer Datenbank und artspezifisch trainierten Genvorhersagemodellen resultierte in 17.338 proteinkodierenden Genen, die etwa 12,5% der geschätzten Genomgröße abdecken. Der Annotation wird u.a. aufgrund beinhaltender Kernrthologen, konservierter Proteindomänenarrangements und der Übereinstimmung mit de novo sequenzierten Peptiden eine hohe Qualität zugesprochen.
Das mapping der Sequenzen von fünf Radix MOTUs gegen die R. auricularia Assemblierung zeigte stark verringerte coverage außerhalb kodierender Bereiche der nicht-Referenz MOTUs aufgrund hoher Nukleotiddiversität. Für 16.039 Gene konnten Topologien berechnet werden und ein Test auf positive Selektion ausgeführt werden. Insgesamt konnte über alle MOTUs hinweg in 678 verschiedenen Genen positive Selektion detektiert werden, wobei jede MOTU ein nahezu einzigartiges Set positiv selektierter Gene beinhaltet. Von allen 16.039 untersuchten Genen konnten 56,4% funktional annotiert werden. Diese niedrige Rate wird vermutlich durch Mangel an genomischer Information in Mollusken verursacht. Anschließende Analysen auf Anreicherungen von Funktionen sind deshalb nur bedingt repräsentativ.
Neben den biologischen Ergebnissen wurden Methoden und Optimierungen genomischer Analysen von Nichtmodellorganismen entwickelt. Dazu zählen eigens angefertigte Skripte, um beispielsweise Transkriptomalignments zu filtern, Trainings eines Genvorhersagemodells automatisiert und parallelisiert auszuführen und Orthogruppen bestimmter Arten aus einer Orthologievorhersage zu extrahieren. Zusätzlich wurden Abläufe entwickelt, um möglichst viele vorhandene Daten in die Assemblierung und Annotation zu integrieren. Etwa wurde ein zusätzliches scaffolding mit eigens assemblierten Transkripten mehrerer MOTUs sequenziell und phylogenetisch begründet ausgeführt.
Insgesamt wird eine umfassende und qualitativ hochwertige Genomsequenz eines Süßwassermollusken präsentiert, welche eine Grundlage für zukünftige Forschungsprojekte z.B. im Bereich der Biodiversität, Populationsgenomik und molekularen Ökologie bietet. Die Ergebnisse dieser Arbeit stellen einen Wissenszuwachs in der Genomik von Mollusken dar, welche bisher trotz ihrer Artenvielfalt deutlich unterrepräsentiert bezüglich assemblierter und annotierter Genome auffallen.
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N2 fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O2 evolution and CO2 fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N2 fixation, H2 metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (−750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
Haloferax volcanii is a well-established model species for haloarchaea. Small scale RNomics and bioinformatics predictions were used to identify small non-coding RNAs (sRNAs), and deletion mutants revealed that sRNAs have important regulatory functions. A recent dRNA-Seq study was used to characterize the primary transcriptome. Unexpectedly, it was revealed that, under optimal conditions, H. volcanii contains more non-coding sRNAs than protein-encoding mRNAs. However, the dRNA-Seq approach did not contain any length information. Therefore, a mixed RNA-Seq approach was used to determine transcript length and to identify additional transcripts, which are not present under optimal conditions. In total, 50 million paired end reads of 150 nt length were obtained. 1861 protein-coding RNAs (cdRNAs) were detected, which encoded 3092 proteins. This nearly doubled the coverage of cdRNAs, compared to the previous dRNA-Seq study. About 2/3 of the cdRNAs were monocistronic, and 1/3 covered more than one gene. In addition, 1635 non-coding sRNAs were identified. The highest fraction of non-coding RNAs were cis antisense RNAs (asRNAs). Analysis of the length distribution revealed that sRNAs have a median length of about 150 nt. Based on the RNA-Seq and dRNA-Seq results, genes were chosen to exemplify characteristics of the H. volcanii transcriptome by Northern blot analyses, e.g. 1) the transcript patterns of gene clusters can be straightforward, but also very complex, 2) many transcripts differ in expression level under the four analyzed conditions, 3) some genes are transcribed into RNA isoforms of different length, which can be differentially regulated, 4) transcripts with very long 5’-UTRs and with very long 3’-UTRs exist, and 5) about 30% of all cdRNAs have overlapping 3’-ends, which indicates, together with the asRNAs, that H. volcanii makes ample use of sense-antisense interactions. Taken together, this RNA-Seq study, together with a previous dRNA-Seq study, enabled an unprecedented view on the H. volcanii transcriptome.
Impaired alveolar formation and maintenance are features of many pulmonary diseases that are associated with significant morbidity and mortality. In a forward genetic screen for modulators of mouse lung development, we identified the non-muscle myosin II heavy chain gene, Myh10. Myh10 mutant pups exhibit cyanosis and respiratory distress, and die shortly after birth from differentiation defects in alveolar epithelium and mesenchyme. From omics analyses and follow up studies, we find decreased Thrombospondin expression accompanied with increased matrix metalloproteinase activity in both mutant lungs and cultured mutant fibroblasts, as well as disrupted extracellular matrix (ECM) remodeling. Loss of Myh10 specifically in mesenchymal cells results in ECM deposition defects and alveolar simplification. Notably, MYH10 expression is downregulated in the lung of emphysema patients. Altogether, our findings reveal critical roles for Myh10 in alveologenesis at least in part via the regulation of ECM remodeling, which may contribute to the pathogenesis of emphysema.
The mechanistic target of rapamycin (mTOR) is elevated in prostate cancer, making this protein attractive for tumor treatment. Unfortunately, resistance towards mTOR inhibitors develops and the tumor becomes reactivated. We determined whether epigenetic modulation by the histone deacetylase (HDAC) inhibitor, valproic acid (VPA), may counteract non-responsiveness to the mTOR inhibitor, temsirolimus, in prostate cancer (PCa) cells. Prostate cancer cells, sensitive (parental) and resistant to temsirolimus, were exposed to VPA, and tumor cell growth behavior compared. Temsirolimus resistance enhanced the number of tumor cells in the G2/M-phase, correlating with elevated cell proliferation and clonal growth. The cell cycling proteins cdk1 and cyclin B, along with Akt-mTOR signaling increased, whereas p19, p21 and p27 decreased, compared to the parental cells. VPA significantly reduced cell growth and up-regulated the acetylated histones H3 and H4. Cdk1 and cyclin B decreased, as did phosphorylated mTOR and the mTOR sub-complex Raptor. The mTOR sub-member Rictor and phosphorylated Akt increased under VPA. Knockdown of cdk1, cyclin B, or Raptor led to significant cell growth reduction. HDAC inhibition through VPA counteracts temsirolimus resistance, probably by down-regulating cdk1, cyclin B and Raptor. Enhanced Rictor and Akt, however, may represent an undesired feedback loop, which should be considered when designing future therapeutic regimens.
Orthologs document the evolution of genes and metabolic capacities encoded in extant and ancient genomes. However, the similarity between orthologs decays with time, and ultimately it becomes insufficient to infer common ancestry. This leaves ancient gene set reconstructions incomplete and distorted to an unknown extent. Here we introduce the "evolutionary traceability" as a measure that quantifies, for each protein, the evolutionary distance beyond which the sensitivity of the ortholog search becomes limiting. Using yeast, we show that genes that were thought to date back to the last universal common ancestor are of high traceability. Their functions mostly involve catalysis, ion transport, and ribonucleoprotein complex assembly. In turn, the fraction of yeast genes whose traceability is not sufficient to infer their presence in last universal common ancestor is enriched for regulatory functions. Computing the traceabilities of genes that have been experimentally characterized as being essential for a self-replicating cell reveals that many of the genes that lack orthologs outside bacteria have low traceability. This leaves open whether their orthologs in the eukaryotic and archaeal domains have been overlooked. Looking at the example of REC8, a protein essential for chromosome cohesion, we demonstrate how a traceability-informed adjustment of the search sensitivity identifies hitherto missed orthologs in the fast-evolving microsporidia. Taken together, the evolutionary traceability helps to differentiate between true absence and nondetection of orthologs, and thus improves our understanding about the evolutionary conservation of functional protein networks. "protTrace," a software tool for computing evolutionary traceability, is freely available at https://github.com/BIONF/protTrace.git; last accessed February 10, 2019.
In times of a growing world population and the associated demand for high crop yield, the understanding and improvement of plant reproduction is of central importance. One key step of plant reproduction is the development of the male gametophyte, which is better known as pollen. In addition, the development of pollen was shown to be very sensitive to abiotic stresses, such as heat, which can cause crop damage and yield loss. To obtain new insights in the development and heat stress response of pollen, a combined transcriptome and proteome analysis was performed for three pollen developmental stages of non- and heat-stressed tomato plants.
The analysis of the transcriptomes of non-stressed pollen developmental stages enabled the determination of mRNAs accumulated in certain developmental stages. The functional analysis of these mRNAs led to the identification of protein families and functional processes that are important at different times of pollen development. A subsequent comparison of the transcriptomes of non- and heat-stressed pollen revealed a core set of 49 mRNAs, which are upregulated in all three developmental stages. The encoded proteins include among other things different heat stress transcription factors and heat shock proteins, which are known key players of the plant heat stress response.
Furthermore, 793 potential miRNAs could be identified in the transcriptome of non- and heat-stressed pollen. Interestingly, 38 out of the 793 miRNAs have already been identified in plants. For more than half of these miRNAs potential target mRNAs were identified and the interactions between miRNAs and mRNAs linked to the development and heat stress response of pollen. In total, 207 developmentally relevant interactions could be determined, out of which 34 have an effect on transcriptional-networks. In addition, 24 of the interactions contribute the heat stress response of pollen, whereby this mainly affects post-meiotic pollen.
An initial correlation of the proteome and transcriptome of the developmental stages revealed that transcriptome analyses are not sufficient to draw exact conclusions about the state of the proteome. A closer look on the relationship of the transcriptome and proteome during pollen development revealed two translational modes that are active during the development of pollen. One mode leads to a direct translation of mRNAs, while the second mode leads a delayed translation at a later point in time. Regarding the delayed translation, it could be shown that this is likely due to a short-term storage of mRNAs in so-called EPPs. The comparison of the proteome and transcriptome response to heat stress revealed that the proteome reacts much stronger and that the reaction is mainly independent from the transcriptome. Finally, the comparison of the proteome of non- and heat-stressed pollen provided first indications for changes in the ribosome composition in response to heat stress, as 57 ribosomal proteins are differentially regulated in at least one developmental stage.
Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila
(2019)
The repeated and improper use of antibiotics had led to an increased number of multiresistant bacteria. Therefore, new lead structures are needed. Here, the synthesis and an expanded structure–activity relationship of the simple and antistaphylococcal amide nematophin from Xenorhabdus nematophila and synthetic derivatives are described. Moreover, the synthesis of intrinsic fluorescent derivatives, incorporating azaindole moieties was achieved for the first time.
Current technologies used to generate CRISPR/Cas gene perturbation reagents are labor intense and require multiple ligation and cloning steps. Furthermore, increasing gRNA sequence diversity negatively affects gRNA distribution, leading to libraries of heterogeneous quality. Here, we present a rapid and cloning-free mutagenesis technology that can efficiently generate covalently-closed-circular-synthesized (3Cs) CRISPR/Cas gRNA reagents and that uncouples sequence diversity from sequence distribution. We demonstrate the fidelity and performance of 3Cs reagents by tailored targeting of all human deubiquitinating enzymes (DUBs) and identify their essentiality for cell fitness. To explore high-content screening, we aimed to generate the largest up-to-date gRNA library that can be used to interrogate the coding and noncoding human genome and simultaneously to identify genes, predicted promoter flanking regions, transcription factors and CTCF binding sites that are linked to doxorubicin resistance. Our 3Cs technology enables fast and robust generation of bias-free gene perturbation libraries with yet unmatched diversities and should be considered an alternative to established technologies.
Numerous cell–cell and cell–matrix interactions within the bone marrow microenvironment enable the controlled lifelong self-renewal and progeny of hematopoietic stem and progenitor cells (HSPCs). On the cellular level, this highly mutual interaction is granted by cell adhesion molecules (CAMs) integrating differentiation, proliferation, and pro-survival signals from the surrounding microenvironment to the inner cell. However, cell–cell and cell–matrix interactions are also critically involved during malignant transformation of hematopoietic stem/progenitor cells. It has become increasingly apparent that leukemia-associated gene products, such as activated tyrosine kinases and fusion proteins resulting from chromosomal translocations, directly regulate the activation status of adhesion molecules, thereby directing the leukemic phenotype. These observations imply that interference with adhesion molecule function represents a promising treatment strategy to target pre-leukemic and leukemic lesions within the bone marrow niche. Focusing on myeloid leukemia, we provide a current overview of the mechanisms by which leukemogenic gene products hijack control of cellular adhesion to subsequently disturb normal hematopoiesis and promote leukemia development.