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Size and shape variation of molar crowns in primates plays an important role in understanding how species adapted to their environment. Gorillas are commonly considered to be folivorous primates because they possess sharp cusped molars which are adapted to process fibrous leafy foods. However, the proportion of fruit in their diet can vary significantly depending on their habitats. While tooth morphology can tell us what a tooth is capable of processing, tooth wear can help us to understand how teeth have been used during mastication. The objective of this study is to explore if differences in diet at the subspecies level can be detected by the analysis of molar macrowear. We analysed a large sample of second lower molars of Grauer’s, mountain and western lowland gorilla by combining the Occlusal Fingerprint Analysis method with other dental measurements. We found that Grauer’s and western lowland gorillas are characterised by a macrowear pattern indicating a larger intake of fruit in their diet, while mountain gorilla’s macrowear is associated with the consumption of more folivorous foods. We also found that the consumption of herbaceous foods is generally associated with an increase in dentine and enamel wear, confirming the results of previous studies.
The Mediterranean fruit fly (medfly), Ceratitis capitata, is an important model organism in biology and agricultural research with high economic relevance. However, information about its embryonic development is still sparse. We share nine long-term live imaging datasets acquired with light sheet fluorescence microscopy (484.5 h total recording time, 373 995 images, 256 Gb) with the scientific community. Six datasets show the embryonic development in toto for about 60 hours at 30 minutes intervals along four directions in three spatial dimensions, covering approximately 97% of the entire embryonic development period. Three datasets focus on germ cell formation and head involution. All imaged embryos hatched morphologically intact. Based on these data, we suggest a two-level staging system that functions as a morphogenetic framework for upcoming studies on medfly. Our data supports research on wild-type or aberrant morphogenesis, quantitative analyses, comparative approaches to insect development as well as studies related to pest control. Further, they can be used to test advanced image processing approaches or to train machine learning algorithms and/or neuronal networks.
Oaks may contribute to the stabilization of European forests under climate change. We utilized two common gardens established in contrasting growth regimes, in Greece (Olympiada) and Germany (Schwanheim), to compare the diurnal photosynthetic performance of a Greek and an Italian provenance of two Mediterranean oaks (Quercus pubescens and Q. frainetto) during the 2019 growing season. Although the higher radiation in the southern common garden led to a strong midday depression of chlorophyll a fluorescence parameters (maximum quantum efficiency of PSII, performance index on absorption basis), comparable light-saturated net photosynthetic rates were achieved in both study areas. Moreover, both species and provenances exhibited analogous responses. Q. pubescens had enhanced chlorophyll a fluorescence traits but similar photosynthetic rates compared to Q. frainetto, whereas the provenances did not differ. These findings indicate the high photosynthetic efficiency of both oaks under the current climate in Central Europe and their suitability for assisted migration schemes.
tRNAs are L-shaped RNA molecules of ~ 80 nucleotides that are responsible for decoding the mRNA and for the incorporation of the correct amino acid into the growing peptidyl-chain at the ribosome. They occur in all kingdoms of life and both their functions, and their structure are highly conserved. The L-shaped tertiary structure is based on a cloverleaf-like secondary structure that consists of four base paired stems connected by three to four loops. The anticodon base triplet, which is complementary to the sequence of the mRNA, resides in the anticodon loop whereas the amino acid is attached to the sequence CCA at the 3′-terminus of the molecule. tRNAs exhibit very stable secondary and tertiary structures and contain up to 10% modified nucleotides. However, their structure and function can also be maintained in the absence of nucleotide modifications. Here, we present the assignments of nucleobase resonances of the non-modified 77 nt tRNAIle from the gram-negative bacterium Escherichia coli. We obtained assignments for all imino resonances visible in the spectra of the tRNA as well as for additional exchangeable and non-exchangeable protons and for heteronuclei of the nucleobases. Based on these assignments we could determine the chemical shift differences between modified and non-modified tRNAIle as a first step towards the analysis of the effect of nucleotide modifications on tRNA’s structure and dynamics.
Natural products have been proven to be important starting points for the development of new drugs. Bacteria in the genera Photorhabdus and Xenorhabdus produce antimicrobial compounds as secondary metabolites to compete with other organisms. Our study is the first comprehensive study screening the anti-protozoal activity of supernatants containing secondary metabolites produced by 5 Photorhabdus and 22 Xenorhabdus species against human parasitic protozoa, Acanthamoeba castellanii, Entamoeba histolytica, Trichomonas vaginalis, Leishmania tropica and Trypanosoma cruzi, and the identification of novel bioactive antiprotozoal compounds using the easyPACId approach (easy Promoter Activated Compound Identification) method. Though not in all species, both bacterial genera produce antiprotozoal compounds effective on human pathogenic protozoa. The promoter exchange mutants revealed that antiprotozoal bioactive compounds produced by Xenorhabdus bacteria were fabclavines, xenocoumacins, xenorhabdins and PAX peptides. Among the bacteria assessed, only P. namnaoensis appears to have acquired amoebicidal property which is effective on E. histolytica trophozoites. These discovered antiprotozoal compounds might serve as starting points for the development of alternative and novel pharmaceutical agents against human parasitic protozoa in the future.
Die oxygene Photosynthese bildet den Grundpfeiler des heutigen Ökosystems unseres Planeten. Neben den gut untersuchten Landpflanzen bilden Mikroalgen eine äußerst bedeutende Organismengruppe der phototrophen Lebewesen. Zu den Mikroalgen zählen die Diatomeen, welche sich beispielsweise durch eine Silikatschale und spezielle Lichtsammelkomplexe auszeichnen und für einen Großteil der marinen Primärproduktion verantwortlich sind. Die stoffwechselphysiologischen Grundlagen des ökologischen Erfolgs der Kieselalgen sind bislang noch unzureichend erforscht. Ein Vertreter der zentrischen Diatomeen, Cyclotella, wurde bereits zur Jahrtausendwende zur biochemischen Charakterisierung der Diatomeen Photosynthese verwendet (Eppard und Rhiel, 1998; Eppard und Rhiel, 2000), das Genom des Organismus aber erst vor kurzem sequenziert (Traller et al., 2016). Die Sequenzierung des Genoms konnte einige Gene für Lichtsammelproteine identifizieren, die Homologie zu den LhcSR-Proteinen aus C. reinhardtii aufweisen, welche nachweislich eine photoprotektive Funktion besitzen (Peers et al., 2009). Diese sogenannten Lhcx-Proteine der Diatomeen sind in den zwei Gruppen der Kieselalgen, den zentrischen und pennaten Diatomeen zu finden, unterscheiden sich aber in ihren jeweiligen Lhcx-Kandidaten. So können in der pennaten Diatomee P. tricornutum vier lhcx-Gene ausgemacht werden, während die zentrische Kieselalge T. pseudonana sechs lhcx-Gene besitzt und C. cryptica vier verschiedene lhcx-Kandidaten genomisch aufweist (Armbrust et al., 2004; Bowler et al., 2008; Traller et al., 2016). Die beschriebenen Diatomeen weisen alle eine Homologie im Lhcx1 auf, während sich die übrigen Lhcx-Kandidaten zwischen pennaten und zentrischen Diatomeen unterscheiden. Ein zwischen T. pseudonana und C. cryptica konserviertes Lhcx ist das Lhcx6_1, welches 2011 das erste Mal massenspektrometrisch an Photosystemen von T. pseudonana nachgewiesen wurde (Grouneva et al., 2011) und in weiteren Massenspektrometrie-gestützten Untersuchungen in beiden zentrischen Diatomeen an Photosynthese-Komplexen gefunden werden konnte (Gundermann et al., 2019; Calvaruso et al., 2020). Die Funktion des Lhcx6_1 ist bislang unklar.
Diese Arbeit konnte das Lhcx6_1 aus C. meneghiniana charakterisieren und Antikörper-gestützt genauer lokalisieren, eine nicht dynamische Phosphorylierung der Thylakoidmembran-Proteine der zentrischen Diatomee nachweisen und die molekularbiologische Zugänglichkeit des Organismus optimieren. qRT-PCR gestützte Expressions-Analysen konnten eine unerwartete Expression des lhcx6_1-Gens aufdecken. Dieses weist, im Vergleich zum Lhcx1, keine Starklicht induzierte Expression auf. Die Expression des Gens konnte nach wenigen Stunden Schwachlicht als maximal bestimmt werden, während sie im Starklicht abnimmt. Das Muster der Genexpression glich im Schwachlicht eher der des lhcf1-Gens. Die Sequenzierung des lhcx6_1 aus C. meneghiniana identifizierte eine verlängerte N-terminale Sequenz des Proteins, welche Homologie zu den minoren Antennen aus A. thaliana besitzt und Teil des reifen Proteins ist. Mittels eines C-terminalen Epitops wurde ein Antikörper gegen das Lhcx6_1 entworfen, welcher das Protein in C. meneghiniana spezifisch nachweisen kann. Die Isolation von Thylakoidmembranen der zentrischen Diatomee und weitergehende Aufreinigung mittels Saccharosedichtegradienten und lpBN-PAGE konnten die Lokalisation des Lhcx6_1 eingrenzen. Das Protein zeigt dabei keine Unterschiede in seiner Lokalisation nach Inkubation in Schwach-, Stark- und Fernrot-Licht und ist vorrangig mit Photosystem I assoziiert. In geringerer Menge konnte es zudem an Photosystem II nachgewiesen werden, während der immunologische Nachweis in Lichtsammelkomplexen (FCPs) minimale Mengen erbrachte. Ferner konnte eine Phosphorylierung des Lhcx6_1 an Threonin-Resten nachgewiesen werden, während die meisten anderen Thylakoidmembran-Proteine mittels Phospho-Serin Antikörper detektiert werden konnten. Weder die Phosphorylierung des Lhcx6_1, noch der anderen Thylakoidmembran-Proteine, zeigt eine dynamische Regulation, im Stile einer state-transition ähnlichen Kinase auf. Die Qualität des Umgebungslichts führte zu keinerlei Unterschieden in Phosphorylierungsmustern. Weiterführende Untersuchungen der Lhcx6_1-Phosphorylierung mittels Phos-tag PAGE identifizieren eine unphosphorylierte und eine einfach phosphorylierte Form des Proteins. Dabei kann an PSI ausschließlich die phosphorylierte Version des Lhcx6_1 gefunden werden. Im Zuge der Arbeit konnte zudem erstmalig die Elektroporation und Konjugation für C. meneghiniana als Transformations-Methoden etabliert werden, während das Protokoll für die biolistische Transformation optimiert wurde. Die Elektroporation erbrachte die höchste Transformationseffizienz. Molekularbiologische Unterfangen eines Lhcx6_1-Knockdowns mittels Antisense-RNA erzielten zunächst, aufgrund der starken Gegenregulation der Diatomee, keinen Erfolg...
Mitochondria are dynamic eukaryotic organelles involved in a variety of essential cellular processes including the generation of adenosine triphosphate (ATP) and reactive oxygen species as well as in the control of apoptosis and autophagy. Impairments of mitochondrial functions lead to aging and disease. Previous work with the ascomycete Podospora anserina demonstrated that mitochondrial morphotype as well as mitochondrial ultrastructure change during aging. The latter goes along with an age-dependent reorganization of the inner mitochondrial membrane leading to a change from lamellar cristae to vesicular structures. Particularly from studies with yeast, it is known that besides the F1Fo-ATP-synthase and the phospholipid cardiolipin also the “mitochondrial contact site and cristae organizing system” (MICOS) complex, existing of the Mic60- and Mic10-subcomplex, is essential for proper cristae formation. In the present study, we aimed to understand the mechanistic basis of age-related changes in the mitochondrial ultrastructure. We observed that MICOS subunits are coregulated at the posttranscriptional level. This regulation partially depends on the mitochondrial iAAA-protease PaIAP. Most surprisingly, we made the counterintuitive observation that, despite the loss of lamellar cristae and of mitochondrial impairments, the ablation of MICOS subunits (except for PaMIC12) leads to a pronounced lifespan extension. Moreover, simultaneous ablation of subunits of both MICOS subcomplexes synergistically increases lifespan, providing formal genetic evidence that both subcomplexes affect lifespan by different and at least partially independent pathways. At the molecular level, we found that ablation of Mic10-subcomplex components leads to a mitohormesis-induced lifespan extension, while lifespan extension of Mic60-subcomplex mutants seems to be controlled by pathways involved in the control of phospholipid homeostasis. Overall, our data demonstrate that both MICOS subcomplexes have different functions and play distinct roles in the aging process of P. anserina.
Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions. We established a fungal culture collection and used Arabidopsis thaliana inoculation bioassays to assess the ability of fungi to facilitate host’s growth in the presence of organic nutrients unavailable to plants. Plant baits captured a representation of fungal communities extant in natural habitats and showed that nutrient limitation has little influence on community assembly. Arabidopsis thaliana inoculated with 31 phylogenetically diverse fungi exhibited a consistent fungus-driven growth promotion when supplied with organic nutrients compared to untreated plants. However, direct phosphorus measurement and RNA-seq data did not support enhanced nutrient uptake but rather that growth effects may result from changes in the plant’s immune response to colonization. The widespread and consistent host responses to fungal colonization suggest that distinct, locally adapted nonmycorrhizal fungi affect plant performance across habitats.
IMPORTANCE: Recent studies have shown that root-associated fungi that do not engage in classical mycorrhizal associations can facilitate the hosts’ access to nutrients in a mycorrhiza-like manner. However, the generality of this capacity remains to be tested. Root-associated fungi are frequently deemed major determinants of plant diversity and performance, but in the vast majority of cases their ecological roles in nature remain unknown. Assessing how these plant symbionts affect plant productivity, diversity, and fitness is important to understanding how plant communities function. Recent years have seen important advances in the understanding of the main drivers of the diversity and structure of plant microbiomes, but a major challenge is still linking community properties with function. This study contributes to the understanding of the cryptic function of root-associated fungi by testing their ability to participate in a specific process: nutrient acquisition by plants.
Myocardial injury as induced by myocardial infarction results in tissue ischemia, which critically incepts cardiomyocyte death. Endothelial cells play a crucial role in restoring oxygen and nutrient supply to the heart. Latest advances in single-cell multi-omics, together with genetic lineage tracing, reveal a transcriptional and phenotypical adaptation to the injured microenvironment, which includes alterations in metabolic, mesenchymal, hematopoietic and pro-inflammatory signatures. The extent of transition in mesenchymal or hematopoietic cell lineages is still debated, but it is clear that several of the adaptive phenotypical changes are transient and endothelial cells revert back to a naïve cell state after resolution of injury responses. This resilience of endothelial cells to acute stress responses is important for preventing chronic dysfunction. Here, we summarize how endothelial cells adjust to injury and how this dynamic response contributes to repair and regeneration. We will highlight intrinsic and microenvironmental factors that contribute to endothelial cell resilience and may be targetable to maintain a functionally active, healthy microcirculation.
Besides transcription, RNA decay accounts for a large proportion of regulated gene expression and is paramount for cellular functions. Classical RNA surveillance pathways, like nonsense-mediated decay (NMD), are also implicated in the turnover of non-mutant transcripts. Whereas numerous protein factors have been assigned to distinct RNA decay pathways, the contribution of long non-coding RNAs (lncRNAs) to RNA turnover remains unknown. Here we identify the lncRNA CALA as a potent regulator of RNA turnover in endothelial cells. We demonstrate that CALA forms cytoplasmic ribonucleoprotein complexes with G3BP1 and regulates endothelial cell functions. A detailed characterization of these G3BP1-positive complexes by mass spectrometry identifies UPF1 and numerous other NMD factors having cytoplasmic G3BP1-association that is CALA-dependent. Importantly, CALA silencing impairs degradation of NMD target transcripts, establishing CALA as a non-coding regulator of RNA steady-state levels in the endothelium.
Specialized surveillance mechanisms are essential to maintain the genetic integrity of germ cells, which are not only the source of all somatic cells but also of the germ cells of the next generation. DNA damage and chromosomal aberrations are, therefore, not only detrimental for the individual but affect the entire species. In oocytes, the surveillance of the structural integrity of the DNA is maintained by the p53 family member TAp63α. The TAp63α protein is highly expressed in a closed and inactive state and gets activated to the open conformation upon the detection of DNA damage, in particular DNA double-strand breaks. To understand the cellular response to DNA damage that leads to the TAp63α triggered oocyte death we have investigated the RNA transcriptome of oocytes following irradiation at different time points. The analysis shows enhanced expression of pro-apoptotic and typical p53 target genes such as CDKn1a or Mdm2, concomitant with the activation of TAp63α. While DNA repair genes are not upregulated, inflammation-related genes become transcribed when apoptosis is initiated by activation of STAT transcription factors. Furthermore, comparison with the transcriptional profile of the ΔNp63α isoform from other studies shows only a minimal overlap, suggesting distinct regulatory programs of different p63 isoforms.
Biosynthesis of butyrate from methanol and carbon monoxide by recombinant Acetobacterium woodii
(2022)
Methanol is one of the most widely produced organic substrates from syngas and can serve as a bio-feedstock to cultivate acetogenic bacteria which allows a major contribution to reducing greenhouse gas. Acetobacterium woodii is one of the very few acetogens that can utilize methanol to produce acetate as sole product. Since A. woodii is genetically tractable, it is an interesting candidate to introduce recombinant pathways for production of bio-commodities from methanol. In this study, we introduced the butyrate production operon from a related acetogen, Eubacterium callanderi KIST612, into A. woodii and show a stable production of butyrate from methanol. This study also reveals how butyrate production by recombinant A. woodii strains can be enhanced with addition of electrons in the form of carbon monoxide. Our results not only show a stable expression system of non-native enzymes in A. woodii but also increase in the product spectrum of A. woodii to compounds with higher economic value.
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
Background: Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read–based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap-closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence.
Findings: Here, we present DENTIST, a sensitive, highly accurate, and automated pipeline method to close gaps in short-read assemblies with long error-prone reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the correct loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks for Drosophila (134 Mb genome), Arabidopsis (119 Mb), hummingbird (1 Gb), and human (3 Gb) and using simulated or real PacBio continuous long reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity.
Conclusion: DENTIST provides an accurate approach to improve the contiguity and completeness of fragmented assemblies with long reads. DENTIST's source code including a Snakemake workflow, conda package, and Docker container is available at https://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are at https://bds.mpi-cbg.de/hillerlab/DENTIST/.
Tick-borne diseases are a major health problem worldwide and could become even more important in Europe in the future. Due to changing climatic conditions, ticks are assumed to be able to expand their ranges in Europe towards higher latitudes and altitudes, which could result in an increased occurrence of tick-borne diseases.
There is a great interest to identify potential (new) areas of distribution of vector species in order to assess the future infection risk with vector-borne diseases, improve surveillance, to develop more targeted monitoring program, and, if required, control measures.
Based on an ecological niche modelling approach we project the climatic suitability for the three tick species Ixodes ricinus, Dermacentor reticulatus and Dermacentor marginatus under current and future climatic conditions in Europe. These common tick species also feed on humans and livestock and are vector competent for a number of pathogens.
For niche modelling, we used a comprehensive occurrence data set based on several databases and publications and six bioclimatic variables in a maximum entropy approach. For projections, we used the most recent IPCC data on current and future climatic conditions including four different scenarios of socio-economic developments.
Our models clearly support the assumption that the three tick species will benefit from climate change with projected range expansions towards north-eastern Europe and wide areas in central Europe with projected potential co-occurrence.
A higher tick biodiversity and locally higher abundances might increase the risk of tick-borne diseases, although other factors such as pathogen prevalence and host abundances are also important.
The toxicity of microplastics on Daphnia magna as key model for freshwater zooplankton is well described. While several studies predict population-level effects based on short-term, individual-level responses, only very few have validated these predictions experimentally. Thus, we exposed D. magna populations to irregular polystyrene microplastics and diatomite as natural particle (both ≤63 µm) over 50 days. We used mixtures of both particle types at fixed particle concentrations (50,000 mL-1) and recorded the overall population density, the size of the individual animals, and resting egg production. Particle exposure adversely affected the population density and structure and induced resting egg production. The terminal population size was 31–42% lower in exposed compared to control populations. Interestingly, mixtures containing diatomite induced stronger effects than microplastics alone highlighting that natural particles are not per se less toxic than microplastics. Our results demonstrate that an exposure to synthetic and natural particles has negative population-level effects on zooplankton. Understanding the mixture toxicity of microplastics and natural particles is important given that aquatic organisms will experience exposure to both. Just as for chemical pollutants, better knowledge of such joint effects is essential to fully understand the environmental risks of complex particle mixtures.
Environmental Implications While microplastics are commonly considered hazardous based on individual-level effects, there is a dearth of information on how they affect populations. Since the latter is key for understanding the environmental impacts of microplastics, we investigated how particle exposures affect the population size and structure of Daphnia magna. In addition, we used mixtures of microplastics and natural particles because neither occurs alone in nature and joint effects can expected in an environmentally realistic scenario. We show that such mixtures adversely affect daphnid populations and highlight that population-level and mixture-toxicity designs are one important step towards more environmental realism in microplastics research.
Exploring the power of moth samples to reveal community patterns along shallow ecological gradients
(2022)
1. Analysing the effects of environmental variation on species assemblages is a key topic in community ecology. However, the outcome may strongly depend on the focal species group. Moths have often been used as the target in ecological studies due to their fast response to environmental change. Yet, some moth subgroups might be more sensitive than others to reflect environmental differences, depending on their functional and physiological characteristics.
2. We investigated which moth subsets are especially suitable to mirror responses to subtle variation in vegetation. We analysed the susceptibility of different subsets to local weather conditions and inter-annual fluctuations. Finally, we checked for the importance of including abundance information. We analysed moth communities (392 species, 23.870 individuals) at 60 sites within two Mediterranean forest reserves and investigated relationships between community composition and environment of (1) all moths (with and without taking abundances into account), and of subsets comprising only (2) small-sized species, (3) host-plant specialists, (4) moss, lichen and detritus feeding species, (5) ‘microlepidoptera’, (6) ‘macro-moths’ and (7) random subsets of 50, 100 and 200 species.
3. Incidence data performed similarly to abundance data in matrix regression models. Host plant specialists responded especially sensitive to small-scaled variation in vegetation composition. Macro-moth samples in contrast were highly prone to local weather conditions and to inter-annual abundance fluctuations. Accordingly, a focus on host-specialists and micro-moths is the best way to analyse relationships between shallow environmental gradients and insect communities.
Acinetobacter baumannii can thrive on a broad range of substrates such as sugars, alcohols, lipids, amino acids and aromatic compounds. The latter three are abundant in the human host and are potential candidates as carbon sources for the metabolic adaptation of A. baumannii to the human host. In this study we determined the biodegradative activities of A. baumannii AYE with monocyclic aromatic compounds. Deletion of genes encoding the key enzymes of the ß-ketoadipate pathway, the protocatechuate-3,4-dioxygenase (ΔpcaHG) and the catechol-1,2-dioxygenase (ΔcatA), led to a complete loss of growth on benzoate and p-hydroxybenzoate, suggesting that these substrates are metabolized via the two distinct branches (pca and cat) of this pathway. Furthermore, we investigated the potential role of these gene products in host adaptation by analyzing the capability of the mutants to resist complement-mediated killing. These studies revealed that the mutants exhibit a decreased complement resistance, but a dramatic increase in survival in normal human serum in the presence of p-hydroxybenzoate or protocatechuate. These results indicate that the ß-ketoadipate pathway plays a role in adaptation of A. baumannii to the human host. Moreover, the single and double mutants exhibited increased antibiotic resistances indicating a link between the two dioxygenases and antibiotic resistance.
The tremendous body of knowledge about genetics, cell biology, and metabolism of Saccharomyces cerevisiae, as well as its long history and robustness in industrial fermentations, have made this yeast one of the most popular microbial cell factories. Novel genetic tools have enabled the rapid construction of strains producing various platform chemicals, fuels, or pharmaceuticals. The relevance of synthetic biology approaches, such as the construction of fully synthetic genomes and artificial cellular compartments are not only relevant for biotechnological applications but can also lead to new insight into basic principles of life.
Energy-conserving dimethyl sulfoxide reduction in the acetogenic bacterium Moorella thermoacetica
(2022)
Moorella thermoacetica is one of the well-studied thermophilic acetogenic bacteria. It grows by oxidation of organic substrates, CO or H2 coupled to CO2 reduction to acetate. Here, we describe that M. thermoacetica can also use dimethyl sulfoxide as terminal electron acceptor. Growth of M. thermoacetica on glucose or H2 + CO2 was stimulated by dimethyl sulfoxide (DMSO). Membranes showed a DMSO reductase activity, that was induced by growing cells in presence of DMSO. The enzyme used reduced anthraquinone-2,6-disulfonate, benzyl- and methyl viologen as electron donor, but not NAD(P)H. Activity was highest at pH 5 and 60°C, the Km for DMSO was 2.4 mM. Potential DMSO reductase subunits were identified by peptide mass fingerprinting; they are encoded in a genomic region that contains three potential dmsA genes, three dmsB genes and one dmsC gene. Transcriptome analysis revealed that two different dmsAB gene clusters were induced in the presence of DMSO. The function of these two and their predicted biochemical features are discussed. In addition, the data are in line with the hypothesis that M. thermoacetica can use DMSO alongside CO2 as electron acceptor and DMSO reduction is catalysed by an energy-conserving, membrane-bound electron transport chain with DMSO as final electron acceptor.
Several clinically used drugs are derived from microorganisms that often produce them via non-ribosomal peptide synthetases (NRPS), giant megasynthases that activate and connect individual amino acids in an assembly line fashion. Since NRPS are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would allow the biotechnological generation of several different peptides including linear, cyclic and further modified derivatives. Here we describe a detailed phylogenetic analysis of several bacterial NRPS that led to the identification of a new recombination breakpoint within the thiolation (T) domain important in natural NRPS evolution. From this an evolutionary-inspired eXchange Unit between T domains (XUT) approach was developed, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as was shown for the specific production of a proteasome inhibitor, designed and assembled from five different NRPS fragments.
Bisphenols and phthalates, chemicals frequently used in plastic products, promote obesity in cell and animal models. However, these well-known metabolism-disrupting chemicals (MDCs) represent only a minute fraction of all compounds found in plastics. To gain a comprehensive understanding of plastics as a source of exposure to MDCs, we characterized the chemicals present in 34 everyday products using nontarget high-resolution mass spectrometry and analyzed their joint adipogenic activities by high-content imaging. We detected 55,300 chemical features and tentatively identified 629 unique compounds, including 11 known MDCs. Importantly, the chemicals extracted from one-third of the products caused murine 3T3-L1 preadipocytes to proliferate, and differentiate into adipocytes, which were larger and contained more triglycerides than those treated with the reference compound rosiglitazone. Because the majority of plastic extracts did not activate the peroxisome proliferator-activated receptor γ and the glucocorticoid receptor, the adipogenic effects are mediated via other mechanisms and, thus, likely to be caused by unknown MDCs. Our study demonstrates that daily-use plastics contain potent mixtures of MDCs and can, therefore, be a relevant yet underestimated environmental factor contributing to obesity.
The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the absence of structure and to the repetitive nature of their primary sequence. IDRs are known to act in concert with the folded domains of N and here we use NMR spectroscopy to identify the priming events of N interacting with a regulatory SARS-CoV-2 RNA element. 13C-detected NMR experiments, acquired simultaneously to 1H detected ones, provide information on the two IDRs flanking the N-terminal RNA binding domain (NTD) within the N-terminal region of the protein (NTR, 1–248). We identify specific tracts of the IDRs that most rapidly sense and engage with RNA, and thus provide an atom-resolved picture of the interplay between the folded and disordered regions of N during RNA interaction.
1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2
(2022)
The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5′- and 3′-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5′-untranslated region (5′-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5′-UUUCGU-3′ hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.
Plastic pollution is a pervasive problem. In the environment, both the physical and chemical aspects of the material contribute to pollution. For instance, discarded plastic is useless waste that is fragmented upon degradation and so-called microplastics <5 mm are formed. Besides, the chemicals added into plastics are usually customized for specific functions, but these can easily transfer from the polymer into an ambient medium. This work examined both of these aspects. Moreover, the question of whether ecotoxicological effects are more likely to appear because of the microparticle properties or the chemicals transferring from the microplastics was addressed. A special focus was laid on the UV-weathering-induced chemical release.
First, conventional and biodegradable plastics made from fossil and bio-based resources were chosen. The different materials (pre-production and recycled pellets as well as final products)were weathered and their leachates evaluated in vitro. The leachates were analyzed with nontarget screening in order to measure the number of transferred chemicals. Plastics identified as toxic were subjected to further investigations in vivo. A biodegradable shampoo bottle was processed to microplastics and the particles’ physical and chemical properties were assessed with the freshwater worm Lumbriculus variegatus. Here, commonly used endpoints such as mortality, reproduction and weight were tested via different exposure routes. Moreover, the freshwater shrimp Neocaridina palmata was exposed to microplastic beads and fragments to clarify if the shape of the particles affects the ingestion and egestion, respectively. Thereafter, two materials that displayed the strongest toxic responses in vitro within the first study were weathered and leached. Finally, the shrimps were exposed to the leachates and the locomotor behavior was used as an ecologically relevant but less frequently studied endpoint.
The results of the studies highlight that plastics are chemically complex mixtures, containing a wide range of chemicals in terms of the number and functionality. These chemicals induced oxidative stress, baseline toxicity and endocrine activities. This shows that pellets represent a processing state that comprises chemically heterogenous materials. Moreover, it was shown that a degradation initiator is not necessarily relevant to trigger inherent substances to leach out from plastics. Despite this, the UV-weathering resulted in increasingly released chemicals and exacerbated the in vitro toxicities. Even plastics assessed as toxicologically harmless prior to weathering released toxic chemical mixtures once they were weathered. One recycled and all of the biodegradable plastics were toxicologically most concerning. This means that such materials are currently not better than conventional, virgin plastics in terms of their toxicity.
To clarify the source of the microplastic toxicity, L. variegatus was exposed to biodegradable microplastics. The particles were ingested by the worms and adversely affected the examined endpoints. In comparison, microplastics that were depleted from their chemicals via a solvent treatment were less toxic. Kaolin as a natural particle control was evaluated alongside and positively affected the weight of the worms. This emphasizes the ecological relevance of fine-sized matter for the test species. The chemicals extracted from the microplastics induced a 100% mortality. A chemical analysis of the material revealed two ecotoxicologically relevant biocides. The physically-mediated effects of the microplastics seemed to be less of a concern for the worms, which is probably linked to their adaptation to high concentrations of naturally occurring particles in the environment. However, the effects related to the chemicals of plastic cannot be ignored, especially for materials that are claimed to be environmentally friendly.
In the third study, the role of the particle shape in the gut passaging of N. palmata was studied. While the particle size was a determinant factor for the ingestion, the ingestion and egestion of the beads and fragments did not differ, respectively. The shrimps ingested less fragments when food was provided than in the absence of food. As for the worms, the shrimps are known to ingest many naturally occurring particles. Their unselective feeding behavior towards the particle shape could indicate that microplastics as a physical pollutant are negligible for the shrimps. That is why the chemicals of the two most toxic in vitro materials were tested with N. palmata. However, no trend towards elevated or reduced movements of the shrimps was observed, even though the leachates contained baseline toxicants. This shows that the in vitro toxicities of plastics are not necessarily indicative for effects to occur at the in vivo level...
Weltweit werden etwa 17% aller Infektionskrankheiten von Vektoren auf den Menschen übertragen. Dabei dienen meist blutsaugende Arthropoden wie Stechmücken, Zecken oder Sandfliegen als Überträger von Bakterien, Viren oder einzelligen Parasiten. Zur letzteren Gruppe gehört auch der protozoische Erreger der Chagas-Krankheit Trypanosoma cruzi. Er wird von hämatophagen Triatominae, einer Unterfamilie der Raubwanzen (Hemiptera: Reduviidae) während der Blutmahlzeit an einem infizierten Säugerwirt aufgenommen, durchläuft komplexe Entwicklungsschritte im intestinalen Trakt der triatominen Insekten und wird anschließend über den Fäzes und Urin der Wanzen abgegeben. Die Infektion des nächsten Wirts erfolgt dann durch das versehentliche Einreiben der Erreger in die Stichwunde oder auf Schleimhäute. Auch eine Infektion über die orale Aufnahme von kontaminierter Nahrung, Mutter-Kind-Infektionen und die Übertragung durch Blutkonserven und Organtransplantate sind möglich. Die Chagas‑Krankheit, oder auch Amerikanische Trypanosomiasis, ist insbesondere in Mittel- und Südamerika verbreitet und betrifft nach Schätzungen der WHO 6 bis 7 Millionen Menschen. Infolge von globaler Immigration und erhöhtem Reiseverkehr treten jedoch in den letzten Jahrzehnten auch vermehrt Fälle in Europa, den USA, Kanada und den westlichen Pazifikstaaten auf. Da dort bislang geeignete Vektoren fehlen, kommt es außerhalb des lateinamerikanischen Kontinents nicht zu vektorübertragenen Infektionen. Dies könnte sich jedoch im Zuge des Klimawandels und einer voranschreitenden Globalisierung ändern, sollte der Ausbreitung der Chagas-Krankheit eine Ausbreitung ihrer triatominen Vektoren folgen.
Inwieweit Triatominae unter heutigen Bedingungen klimatisch geeignete Habitate außerhalb des amerikanischen Kontinents finden, wurde innerhalb des ersten Projekts der vorliegenden Dissertation untersucht. Dazu wurde mit Hilfe der ökologischen Nischenmodellierung und Vorkommensdaten verschiedener vektorkompetenter Raubwanzenarten sowie klimatischer Umweltvariablen die klimatische Eignung verschiedenster Lebensräume modelliert und global projiziert. Es zeigte sich, dass insbesondere tropische und subtropische Gebiete Afrikas sowie Ost- und Südostasiens zwischen 21° nördlicher Breite und 24° südlicher Breite für viele triatomine Vektorarten geeignete Bedingungen aufweisen. Auffällig ist dabei insbesondere die Art Triatoma rubrofasciata, welche nachweislich bereits in Südchina, Vietnam und weiteren Ländern Afrikas und Asiens gefunden wurde. Die Modellierung
offenbarte, dass weitere ausgedehnte Teile der Küstenregionen Afrikas und Südostasiens als für T. rubrofasciata klimatisch geeignet angesehen werden müssen. Eine weitere Ausbreitung dieser Art ist demnach äußerst wahrscheinlich und stellt bislang das größte Risiko autochthon übertragener Chagas-Infektionen außerhalb des amerikanischen Kontinents dar. Es konnten außerdem zwei triatomine Arten identifiziert werden, namentlich T. infestans und T. sordida, welche in gemäßigten Klimazonen geeignete Habitate finden. Zu diesen gehören beispielsweise Neuseeland und Teile Australiens, aber auch südeuropäische Länder wie Spanien, Italien, Griechenland und Portugal. Da mit einer Ausweitung der klimatisch geeigneten Gebiete infolge des sich verändernden Klimas zu rechnen ist, wäre ein Monitoring der Vektoren, wie es bereits in Südchina etabliert ist, aber insbesondere die Einführung der Meldepflicht für Amerikanische Trypanosomiasis in diesen Regionen sinnvoll. Die Ergebnisse der Studie zeigen deutlich, dass die bisher vernachlässigte Tropenkrankheit Chagas nicht allein ein Problem des lateinamerikanischen Kontinents ist, sondern deren Erforschung vielmehr weltweit Beachtung finden sollte.
So konzentrierten sich die folgenden Forschungsprojekte der Promotion verstärkt auf die Mechanismen, welche die Entwicklung und Transmission des Parasiten und die Interaktion mit seinen Vektoren betreffen. Von besonderem Interesse waren dabei die ökologischen Prozesse, welche bei der Kolonisation des Darmtrakts der Vektoren durch T. cruzi ablaufen und essentiell für die Proliferation und damit die Übertragung des Parasiten sind. Eine entscheidende Rolle spielen dabei die mit dem Vektor assoziierten Mikroorganismen und ihre funktionellen Fähigkeiten – zusammengefasst als Mikrobiom bezeichnet. Dieses erfüllt wichtige physiologische Funktionen des Insekts und kann beispielsweise das Immunsystem und die Detoxifikation beeinflussen. Um die Veränderungen der organismischen Zusammensetzung und der funktionellen Kapazitäten, welche die Infektion mit dem Pathogen im Darmtrakt der Vektoren auslösen, zu untersuchen, wurde ein metagenomischer Shotgun Sequenzierungsansatz gewählt. Die daraus resultierenden Datensätze wurden anschließend bioinformatisch ausgewertet und auf ihre mikrobielle Zusammensetzung und metabolischen Fähigkeiten hin untersucht. Es zeigte sich zunächst, dass das Bakterium Rhodococcus rhodnii, welches lange als alleiniger echter Symbiont des untersuchten Vektors Rhodnius prolixus galt, in seiner Funktionalität nicht einzigartig im Mikrobiom des Insekts ist. ...
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
The brains of black 6 mice (Mus musculus) and Seba’s short-tailed bats (Carollia perspicillata) weigh roughly the same and share the mammalian neocortical laminar architecture. Bats have highly developed sonar calls and social communication and are an excellent neuroethological animal model for auditory research. Mice are olfactory and somatosensory specialists and are used frequently in auditory neuroscience, particularly for their advantage of standardization and genetic tools. Investigating their potentially different general auditory processing principles would advance our understanding of how the ecological needs of a species shape the development and function of the mammalian nervous system. We compared two existing datasets, recorded with linear multichannel electrodes down the depth of the primary auditory cortex (A1) while awake, across both species while presenting repetitive stimulus trains with different frequencies (∼5 and ∼40 Hz). We found that while there are similarities between cortical response profiles in bats and mice, there was a better signal to noise ratio in bats under these conditions, which allowed for a clearer following response to stimuli trains. This was most evident at higher frequency trains, where bats had stronger response amplitude suppression to consecutive stimuli. Phase coherence was far stronger in bats during stimulus response, indicating less phase variability in bats across individual trials. These results show that although both species share cortical laminar organization, there are structural differences in relative depth of layers. Better signal to noise ratio in bats could represent specialization for faster temporal processing shaped by their individual ecological niches.
Motivation Expert curation to differentiate between functionally diverged homologs and those that may still share a similar function routinely relies on the visual interpretation of domain architecture changes. However, the size of contemporary data sets integrating homologs from hundreds to thousands of species calls for alternate solutions. Scoring schemes to evaluate domain architecture similarities can help to automatize this procedure, in principle. But existing schemes are often too simplistic in the similarity assessment, many require an a-priori resolution of overlapping domain annotations, and those that allow overlaps to extend the set of annotations sources cannot account for redundant annotations. As a consequence, the gap between the automated similarity scoring and the similarity assessment based on visual architecture comparison is still too wide to make the integration of both approaches meaningful.
Results Here, we present FAS, a scoring system for the comparison of multi-layered feature architectures integrating information from a broad spectrum of annotation sources. Feature architectures are represented as directed acyclic graphs, and redundancies are resolved in the course of comparison using a score maximization algorithm. A benchmark using more than 10,000 human-yeast ortholog pairs reveals that FAS consistently outperforms existing scoring schemes. Using three examples, we show how automated architecture similarity assessments can be routinely applied in the benchmarking of orthology assignment software, in the identification of functionally diverged orthologs, and in the identification of entries in protein collections that most likely stem from a faulty gene prediction.
Untersuchungen zur Bedeutung selektiver Autophagie für Alterungsprozesse von Podospora anserina
(2022)
Das Ziel der vorliegenden Arbeit war, die Funktion und die Rolle von Autophagie-assoziierten Proteinen im Alternsmodell Podospora anserina zu untersuchen und einen Einblick in die nicht-selektive Autophagie, die Mitophagie und die Bildung und den Abbau von Autophagosomen im Zusammenhang zur Alterung von P. anserina zu analysieren. Dabei wurden folgende Erkenntnisse erhalten:
1. Die Untersuchungen zu ΔPaAtg8 bestätigen, dass die PaATG8-abhängige Autophagosomenbildung zur Aufrechterhaltung der Lebensspanne benötigt wird. In ΔPaAtg8 kommt es zu einem Verlust der nicht-selektiven Autophagie. Die Mitophagie hingegen ist auch ohne PaATG8 partiell möglich und es liegt ein PaATG8-unabhängiger Abbau von mitochondrialen Proteinen in P. anserina vor.
2. In P. anserina ist PaATG11 an der nicht-selektiven Autophagie beteiligt und auch die Mitophagie erfolgt in Abhängigkeit dieses Gerüstproteins. Während der PaAtg11-Deletionsstamm unter Normalbedingungen keinen zum Wildtyp veränderten Phänotyp zeigt, führt eine Kultivierung auf M2-Medium mit Glycerin als einziger Kohlenstoffquelle zu einer starken Verkürzung der Lebensspanne. Eine mikroskopische Untersuchung der Mitochondrien zeigte, dass im juvenilen Altersstadium von ΔPaAtg11 stark fragmentierte Mitochondrien vorliegen. Während der Alterung normalisiert sich die Mitochondrienmorphologie wieder. Der mitochondriale Funktionsverlust wird möglicherweise von den fragmentierten Mitochondrien ausgelöst, denn eine Kultivierung von älteren ΔPaAtg11-Stämmen auf M2-Medium mit Glycerin führt zu einer Normalisierung der Lebensspanne.
3. Die initialen Untersuchungen zur ΔPaAtg11/ΔPaAtg24-Doppelmutante zeigen, dass es bei der Kultivierung unter Normalbedingungen zu einem additiven Effekt der beiden Genverluste kommt. Bei der Anzucht auf M2-Medium mit Glycerin hingegen kann eine im Vergleich zum ΔPaAtg11-Stamm längere Lebensspanne festgestellt werden. Die Mikroskopie der Mitochondrien in ΔPaAtg11/ΔPaAtg24 zeigt, dass im juvenilen Alter zum Wildtyp vergleichbare filamentöse Mitochondrien vorhanden sind.
4. In P. anserina ist PaATG24 kein Mitophagierezeptorprotein, da im PaAtg24-Deletionsstamm eine Beeinträchtigung der nicht-selektiven Autophagie vorliegt. Auch die Mitophagie ist in diesem Stamm geschädigt. Die mikroskopische Betrachtung der Mitochondrien zeigt keinen Unterschied zum Wildtyp. Bei der Untersuchung zur Mitochondrienfunktion durch M2-Medium mit Glycerin ist wie unter Normalbedingungen eine verkürzte Lebensspanne feststellbar.
5. Der Abbau von GFP::PaATG8 ist in der PaAtg24-Deletionsmutante signifikant verringert und es kommt zu einer Akkumulation von Autophagosomen, somit liegt in diesem Stamm eine Beeinträchtigung des autophagosomalen Flusses vor. Bei der mikroskopischen Untersuchung von PaATG24 zeigt sich, dass dieses Protein in P. anserina im Bereich der Vakuolen lokalisiert ist. Die Analyse der Vakuole-Autophagosomen-Fusion zeigt jedoch, dass dieser Mechanismus unabhängig von PaATG24 ist. Die Vakuolenmorphologie und Vakuolengröße ist in ΔPaAtg24 beeinträchtigt und dadurch kommt es zu dem beobachteten Defekt der nicht-selektiven und selektiven Autophagie.
Although new advances in neuroscience allow the study of vocal communication in awake animals, substantial progress in the processing of vocalizations has been made from brains of anaesthetized preparations. Thus, understanding how anaesthetics affect neuronal responses is of paramount importance. Here, we used electrophysiological recordings and computational modelling to study how the auditory cortex of bats responds to vocalizations under anaesthesia and in wakefulness. We found that multifunctional neurons that process echolocation and communication sounds were affected by ketamine anaesthesia in a manner that could not be predicted by known anaesthetic effects. In wakefulness, acoustic contexts (preceding echolocation or communication sequences) led to stimulus-specific suppression of lagging sounds, accentuating neuronal responses to sound transitions. However, under anaesthesia, communication contexts (but not echolocation) led to a global suppression of responses to lagging sounds. Such asymmetric effect was dependent on the frequency composition of the contexts and not on their temporal patterns. We constructed a neuron model that could replicate the data obtained in vivo. In the model, anaesthesia modulates spiking activity in a channel-specific manner, decreasing responses of cortical inputs tuned to high-frequency sounds and increasing adaptation in the respective cortical synapses. Combined, our findings obtained in vivo and in silico reveal that ketamine anaesthesia does not reduce uniformly the neurons’ responsiveness to low and high frequency sounds. This effect depends on combined mechanisms that unbalance cortical inputs and ultimately affect how auditory cortex neurons respond to natural sounds in anaesthetized preparations.
Heart development is a dynamic process modulated by various extracellular and intracellular cues. Cardiac progenitors in vertebrates such as the zebrafish, migrate over to the midline after differentiation from the epiblast (Bakkers, 2011; Rosenthal & Harvey, 2010; Stainier et al., 1996; Trinh & Stainier, 2004). These progenitors form a cardiac disc at the midline which elongates into the linear heart tube. The differentiation and migration of cardiac precursors is modulated by signaling interactions between cardiac precursor cells and their extracellular environment known as the Extracellular Matrix (ECM). Studies have shown that Cell-ECM interactions play a crucial role in sculpting the heart during early morphogenic events (Davis CL, 1924; Männer & Yelbuz, 2019; Rosenthal & Harvey, 2010). One key factor to these processes is the presence of a specialized ECM known as the Basement Membrane (BM). Extracellular basement membrane proteins such as Fibronectin have been shown to modulate these very early migration processes of the cardiomyocyte progenitors (Trinh & Stainier, 2004). As the heart develops further, the linear heart tube is composed of myocardial cells with an inner endothelial cell lining separated by a layer of thick jelly like substance called the cardiac jelly (Barry A, 1948; Davis CL, 1924; Little et al., 1989). The cardiac jelly also called the cardiac basement membrane, has been shown to regulate distinct developmental events during cardiogenesis. This early CJ contains components of the basal lamina such as laminins, fibronectin, hyaluronan as well as non-fibrillar collagens such as Collagen IV (Little et al., 1989). In this study, I aimed to identify ECM molecules of the Basement Membrane in the heart and identify their role in the modulation of cardiac development and regeneration using the zebrafish as my model organism.
I identified genes belonging to the Zebrafish Matrisome expressed during cardiac developmental and regeneration and performed CRISPR/Cas9 sgRNA mediated mutagenesis. I also developed overexpression tools for these genes.
Agrinp168 mutants exhibited no obvious gross morphology defects during cardiac development and were adult viable. Adult mutants exhibited reduced cardiomyocyte proliferation, but no significant difference in cardiomyocyte dedifferentiation post cardiac cryoinjury.
Decorin overexpression through mRNA injections led to increased myocardial wall thickness and DN dcn overexpression through mRNA injections led to loss of cardiac looping during early development.
Mutants for Small Leucine Rich Proteoglycan (SLRP) prelp generated using CRISPR/Cas9 mutagenesis exhibited cardiovascular defects. Close observation of prelp mutant hearts revealed a reduced heart rate and impaired fractional shortening of the ventricle. prelp mutants exhibited an enlarged atrium at 48 hpf and 72 hpf as well as a reduced ventricle size at 72 hpf. Chamber size in the mutant hearts were enlarged irrespective of contractility of the heart. Mutants showed an increased number of Atrial cardiomyocytes, but no change in cell size. On the molecular level, extracellular Laminin localization was disrupted in prelp mutants along with an increase in thickness and volume of the cardiac HA in the CJ suggesting a potential compensatory role, or retention of immaturity of the cardiac jelly in the prelp mutants. Transcriptomics analysis on the prelp mutant hearts revealed downregulation of ECM organization and ECM-Receptor interaction processes in the mutants. Gene Ontology analysis on prelp mutants hearts transcriptome revealed increased MAPK signaling. Interestingly, genes related to degradation of cardiac HA and maturation of cardiac jelly were downregulated, and genes related to epithelial identity of cardiomyocytes were upregulated. Analysis of the mutant hearts at single cell resolution revealed increased number of mutants exhibiting rounded up cardiomyocytes and loss of apical Podocalyxin. Truncated forms of prelp were generated to identify domain specific roles for Prelp, and reintroduction of N-terminal truncated Prelp into the mutants rescued the basal lamina localization and cardiac jelly volume phenotypes. Myocardium specific re-establishment of prelp expression revealed a marked rescue of the mutant cardiovascular phenotype suggesting that tissue specific expression of prelp is not required so long as Prelp is secreted into the CJ. With these data, I’ve elucidated the role of ECM SLRPs in modulation of cardiac chamber morphogenesis process and regeneration of the heart.
Many clinically used drugs are derived from or inspired by bacterial natural products that often are biosynthesised via non-ribosomal peptide synthetases (NRPS), giant megasynthases that activate and join individual amino acids in an assembly line fashion. Since NRPS are not limited to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would allow the biotechnological generation of complex peptides including linear, cyclic and further modified natural product analogues, e.g. to optimise natural product leads. Here we describe a detailed phylogenetic analysis of several bacterial NRPS that led to the identification of a new recombination breakpoint within the thiolation (T) domain that is important for natural NRPS evolution. From this, an evolution-inspired eXchange Unit between T domains (XUT) approach was developed which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Calcium (Ca2+) elevation is an essential secondary messenger in many cellular processes, including disease progression and adaptation to external stimuli, e.g., gravitational load. Therefore, mapping and quantifying Ca2+ signaling with a high spatiotemporal resolution is a key challenge. However, particularly on microgravity platforms, experiment time is limited, allowing only a small number of replicates. Furthermore, experiment hardware is exposed to changes in gravity levels, causing experimental artifacts unless appropriately controlled. We introduce a new experimental setup based on the fluorescent Ca2+ reporter CaMPARI2, onboard LED arrays, and subsequent microscopic analysis on the ground. This setup allows for higher throughput and accuracy due to its retrograde nature. The excellent performance of CaMPARI2 was demonstrated with human chondrocytes during the 75th ESA parabolic flight campaign. CaMPARI2 revealed a strong Ca2+ response triggered by histamine but was not affected by the alternating gravitational load of a parabolic flight.
Animals use the geomagnetic field and astronomical cues to obtain compass information. The magnetic compass is not a uniform mechanism, as several functional modes have been described in different animal groups. The Sun compass requires the internal clock to interpret the position of the Sun. For star compass orientation, night-migrating birds seem to use the star pattern as a whole, without involving the internal clock. Both the astronomical compass mechanisms are based on learning processes to adapt them to the geographic latitude where the animals live and, in long-living animals, to compensate for the seasonal changes. Several mechanisms are used to determine the compass course to a goal. Using information collected during the outward journey is mostly done by path integration: recording the direction with a compass and integrating its twists and turns. Migratory animals have innate programs to guide them to their still unknown goal. Highly mobile animals with large ranges develop a so-called navigational ‘map’, a mental representation of the spatial distribution of navigational factors within their home region and their migration route. The nature of the factors involved is not yet entirely clear; magnetic intensity and inclination are the ones best supported so far.
Kálmán Vánky (15th of June 1930–18th of October 2021) was arguably the most prolific researcher of smut fungi so far. He published more than 1000 taxonomic novelties, and crowned his outstanding oeuvre with the most comprehensive monograph of the smut fungi (Smut Fungi of the World) written to date.
Previous studies towards reduced oxygen availability have mostly focused on changes in total mRNA expression, neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic episodes often persist for prolonged periods, we further compared the adaptation to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short-term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to a compensatory attenuation of immune responses, but also, most notably, to the reduction in nuclear-encoded mRNAs associated with various mitochondrial functions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for the rapid recovery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive resource of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we uncover that RNA stability regulation controls mitochondrial functions in the context of hypoxia.
Energy-converting hydrogenases (Ech) are ancient, membrane-bound enzymes that use reduced ferredoxin (Fd) as an electron donor to reduce protons to molecular H2. Experiments with whole cells, membranes and vesicle-fractions suggest that proton reduction is coupled to proton translocation across the cytoplasmatic membrane, but this has never been demonstrated with a purified enzyme. To this end, we produced a His-tagged Ech complex in the thermophilic and anaerobic bacterium Thermoanaerobacter kivui. The enzyme could be purified by affinity chromatography from solubilized membranes with full retention of its eight subunits, as well as full retention of physiological activities, i.e., H2-dependent Fd reduction and Fd2--dependent H2 production. We found the purified enzyme contained 34.2 ± 12.2 mol of iron/mol of protein, in accordance with seven predicted [4Fe-4S]-clusters and one [Ni-Fe]-center. The pH and temperature optima were at 7 to 8 and 66 °C, respectively. Notably, we found that the enzymatic activity was inhibited by N,N′-dicyclohexylcarbodiimide, an agent known to bind ion-translocating glutamates or aspartates buried in the cytoplasmic membrane and thereby inhibiting ion transport. To demonstrate the function of the Ech complex in ion transport, we further established a procedure to incorporate the enzyme complex into liposomes in an active state. We show the enzyme did not require Na+ for activity and did not translocate 22Na+ into the proteoliposomal lumen. In contrast, Ech activity led to the generation of a pH gradient and membrane potential across the proteoliposomal membrane, demonstrating that the Ech complex of T. kivui is a H+-translocating, H+-reducing enzyme.
Acetogenic bacteria such as Acetobacterium woodii use the Wood–Ljungdahl pathway (WLP) for fixation of CO2 and energy conservation. This pathway enables conversion of diverse substrates to the main product of acetogenesis, acetate. Methyl group containing substrates such as methanol or methylated compounds, derived from pectin, are abundant in the environment and a source for CO2. Methyl groups enter the WLP at the level of methyltetrahydrofolic acid (methyl-THF). For methyl transfer from methanol to THF a substrate-specific methyltransferase system is required. In this study, we used genetic methods to identify mtaBC2A (Awo_c22760-Awo_c22740) as the methanol-specific methyltransferase system of A. woodii. After methyl transfer, methyl-THF serves as carbon and/or electron source and the respiratory Rnf complex is required for redox homeostasis if methanol + CO2 is the substrate. Resting cells fed with methanol + CO2, indeed converted methanol to acetate in a 4:3 stoichiometry. When methanol was fed in combination with other electron sources such as H2 + CO2 or CO, methanol was converted Rnf-independently and the methyl group was condensed with CO to build acetate. When fed in combination with alternative electron sinks such as caffeate methanol was oxidized only and resulting electrons were used for non-acetogenic growth. These different pathways for the conversion of methyl-group containing substrates enable acetogens to adapt to various ecological niches and to syntrophic communities.
Forest species are affected by macroclimate, however, the microclimatic variability can be more extreme and change through climate change. Fungal fruiting community composition was affected by microclimatic differences. Here we ask whether differences in the fruiting community can be explained by morphological traits of the fruit body, which may help endure harsh conditions. We used a dead wood experiment and macrofungal fruit body size, color, and toughness. We exposed logs of two host tree species under closed and experimentally opened forest canopies in a random-block design for four years and identified all visible fruit bodies of two fungal lineages (Basidio- and Ascomycota). We found a consistently higher proportion of tough-fleshed species in harsher microclimates under open canopies. Although significant, responses of community fruit body size and color lightness were inconsistent across lineages. We suggest the toughness-protection hypothesis, stating that tough-fleshed fruit bodies protect from microclimatic extremes by reducing dehydration. Our study suggests that the predicted increase of microclimatic harshness with climate change will likely decrease the presence of soft-fleshed fruit bodies. Whether harsh microclimates also affect the mycelium of macrofungi with different fruit body morphology would complement our findings and increase predictability under climate change.
Autism spectrum disorder (ASD) is a common neurodevelopmental disorder with a multifarious clinical presentation. Even though many genetic risk factors have been identified and studied in mouse models, the neurophysiological mechanisms underlying the autistic phenotype are still unclear. Based on the high rates of comorbidity with epilepsy, it was hypothesized that the balance between excitation and inhibition in neural circuits may be disrupted in autistic individuals.
In this dissertation, synaptic and network activity was measured in three different genetically modified mouse models that exhibit the characteristic behavioral abnormalities of the disorder: the Neurobeachin (Nbea) haploinsufficient mouse, the Neuroligin-3 (Nlgn3) knockout (KO) mouse, and the Neuroligin-4 (Nlgn4) KO mouse. Each of the affected proteins is involved in the formation and/or function of synapses in the central nervous system. Therefore, it was posited that the reduction or deletion of these proteins might alter the balance of excitatory to inhibitory synaptic transmission in individual neurons and in neural circuits. Extracellular recordings in the hippocampal dentate gyrus of anesthetized mice revealed that the excitation-inhibition (E-I) balance was reduced in Nbea haploinsufficient and Nlgn4 KO mice, but unchanged in Nlgn3 KO mice despite a reduction in excitatory synaptic transmission to dentate granule cells. Unexpectedly, the intrinsic excitability of dentate granule cells was altered in all three mouse models. These results imply that a homeostatic increase in the intrinsic excitability is able to compensate for the decreased excitatory transmission in Nlgn3 KO mice, whereas the decreased intrinsic excitability in the Nbea haploinsufficient and Nlgn4 KO mice leads to a reduction in the E-I balance. Taken together, these findings suggest that the influence of genetic factors on the E-I balance might be a potential common mechanism underlying the development of ASD.
Echolocation behavior, a navigation strategy based on acoustic signals, allows scientists to explore neural processing of behaviorally relevant stimuli. For the purpose of orientation, bats broadcast echolocation calls and extract spatial information from the echoes. Because bats control call emission and thus the availability of spatial information, the behavioral relevance of these signals is undiscussable. While most neurophysiological studies, conducted in the past, used synthesized acoustic stimuli that mimic portions of the echolocation signals, recent progress has been made to understand how naturalistic echolocation signals are encoded in the bat brain. Here, we review how does stimulus history affect neural processing, how spatial information from multiple objects and how echolocation signals embedded in a naturalistic, noisy environment are processed in the bat brain. We end our review by discussing the huge potential that state-of-the-art recording techniques provide to gain a more complete picture on the neuroethology of echolocation behavior.
Chemical pollution is one of the main contributors to the degradation of lotic ecosystems and their biodiversity. Among chemicals driving lotic biodiversity decline are anthropogenic organic micropollutants (AOM), which affect the survival and functioning of freshwater organisms. Continuous exposure of freshwater organisms to AOM leads to adverse effects that sometimes cannot be traced with standard toxicity methods such as standard toxicity testing or biodiversity indices. Among these effects of AOM are selective or mutagenic effects that cause impaired species genetic diversity. Thus, the correlation between different levels of AOM and genetic diversity of species is still poorly understood. However, it can be explored by applying population genetics screening.
In Chapter 1 of this thesis, background information on environmental pollution, genetic screening, and the detection of evolutionary-relevant AOM effects in freshwater organisms are described and the thesis goals are identified. The main goal of the thesis is to study whether AOM exposure occurring in European rivers causes a significant evolutionary footprint in freshwater species and leads to a selection of more tolerant geno-and phenotypes. Therefore, population genetics indices together with high-resolution chemical exposure screening of a widespread indicator invertebrate species, Gammarus pulex (Linnaeus, 1758), living in polluted and pristine European rivers were investigated.
In Chapter 2, the development of a genetic screening method for G. pulex (microsatellites) is described. Due to genetic differentiation and the presence of morphologically cryptic lineages, the available sets of target loci do not enable a reliable population genetic characterization of G. pulex from central Germany. Thus, a novel set of microsatellite loci for a high-precision assessment of population genetic diversity was here applied. Eleven loci were first identified and thereafter amplified in G. pulex from three rivers. The new loci reliably amplified and indicated polymorphisms in the studied amphipods. The amplification resulted in the successful identification of genetically distinct populations of G. pulex from the analyzed rivers. Moreover, the microsatellite loci were amplified in other genetic lineages of G. pulex and another Gammarus species, G. fossarum, promising a broader applicability of the loci in related amphipod species.
In Chapter 3, the effects of AOM on species genetic differentiation and sensitivity to toxic chemicals in a typical central European river with pristine and AOM-polluted sections was investigated. The river’s site-specific concentrations of AOM were assessed by chemical analysis of G. pulex tissue and water samples. To test, whether different levels of AOM in the river select for pollution-dependent genotypes, the genetic structure of G. pulex from the river was analyzed. Finally, the toxicokinetics of and sensitivity to the commonly used insecticide imidacloprid were determined for amphipods sampled at pristine and polluted sections to assess whether various levels of AOM in the river influence sensitivity of G. pulex to imidacloprid. The results indicated that different levels of AOM did not drive genetic divergence of G. pulex within the river but led to an increased sensitivity of exposed amphipods to imidacloprid. The amphipods living in polluted river sections were more sensitive to the insecticide due to chronic exposure to toxic levels of AOM.
In Chapter 4, the relationship between site-specific pollution levels of AOM and genetic diversity parameters of G. pulex was analyzed at the regional scale within six rivers in central Germany. The genetic structure of G. pulex in the studied area was tested for relatedness to the waterway distance between sites. Gammarus pulex genetic diversity parameters, including allelic richness and inbreeding rate, were tested against environmental pollution parameters using linear mixed-effect- and structural-equation models. According to the results, G. pulex genetic diversity parameters were significantly associated with the detected AOM levels. At sites with high concentrations of AOM and toxicity potential G. pulex showed reduced genetic diversity and increased rates of inbreeding. These results suggest that AOM play a major role in shaping the genetic diversity of G. pulex in rivers.
According to the findings presented here, the applied microsatellites can be used to successfully detect changes in genetic patterns in freshwater amphipods facing increased levels of AOM. The findings indicate that levels of AOM representative for European rivers do not lead to the separation of genotypes among G. pulex as the connectivity between sites majorly contributes to species’ genetic structure. However, the chronic exposure to increased levels of toxic AOM leads to a reduction of species genetic diversity and increases the sensitivity of G. pulex to the toxic chemical effects.
A promising strategy to reduce the dependency from fossil fuels is to use the yeast Saccharomyces cerevisiae to bioconvert renewable non-food feedstocks or waste streams, like lignocellulosic biomass, into bioethanol and other valuable molecule blocks. Lignocellulosic feedstocks contain glucose and significant fractions of the pentoses xylose and arabinose in varying proportions depending on the biomass type. S. cerevisiae is an efficient glucose consumer, but it cannot metabolize xylose and arabinose naturally. Therefore, extensive research using recombinant DNA techniques has been conducted to introduce and improve the biochemical pathways necessary to utilize these non-physiological substrates. However, any functional pathway capable of metabolizing D xylose and L arabinose in S. cerevisiae requires the transport of these sugars across the plasma membrane. The endogenous sugar transport system of S. cerevisiae can conduct a limited uptake of D-xylose and L-arabinose; this uptake enables only basal growth when the enzymatic pathways are provided. For this reason, the uptake of D xylose and L-arabinose has been recognized as a limiting step for the efficient utilization of these non-physiological substrates.
Gal2, a member of the major facilitator superfamily, is one of the most studied hexose transporters in S. cerevisiae. Although its expression is repressed in the presence of glucose, it also transports this sugar with high affinity when constitutively expressed. Recent efforts to engineer yeast strains for the utilization of plant biomass have unraveled the ability of Gal2 to transport non-physiological substrates like xylose and arabinose, among others. Improving Gal2 kinetic and substrate specificity, particularly for pentoses, has become a crucial target in strain engineering. The main goal of this study is to improve the utilization of xylose and arabinose by increasing the cell permeability of these non physiological substrates through the engineering of the galactose permease Gal2.
GAL2 gene expression depends on galactose, which acts as an inducer; nevertheless, even in the presence of galactose, glucose act as a strict repressor; consequently, GAL2 gene is usually placed under the control of a constitutive promoter. However, the presence of glucose additionally triggers the Gal2 degradation, which is mediated by the covalent attachment of the small 76 amino acid protein ubiquitin (Ub) to the targeted transporter; in a multi-step process called ubiquitination.
Ubiquitination of hexose permeases involves the activation of the Ub molecule by the E1 Ub-activating enzyme using ATP; then, the activated Ub is transferred to a specific Ub-conjugating enzyme E2, which donates the Ub indirectly through a specific HECT E3 enzyme (Rsp5) to a lysine residue of the substrate, with the aid of an adaptor protein which recognizes the target (Rsp5-adaptor). Ubiquitinated permeases are sent by membrane invagination to early endosomes, where they encounter ESCRTs (endosomal sorting complex required for transport). The targeted permeases are sorted in intralumenal vesicles (ILV) inside of the endosome, which after several cycles, turns into a multivesicular body (MVB) that subsequently fuses with the vacuole to expose the protein content of the ILVs to lumenal hydrolases for degradation.
Gal2 contains 30 lysine residues that may accept the ubiquitin molecule, which targets its degradation. It is known that mono-ubiquitination by Rsp5 on multiple lysine residues is necessary to internalize Gal2 (Horak & Wolf, 2001). However, the authors did not identify the specific lysine residues involved in the ubiquitination processes. This study screened several Gal2 variants where lysine residues were mutated or removed from the protein sequence to discover which lysine residues are likely involved in ubiquitination and consequent turnover of the transporter. The results of the screening showed that mutation of the N terminal lysine residues 27, 37, and 44 to arginine (Gal23KR) produced a functional transporter that, when fused with GFP (Gal23KR_GFP), showed an exclusive localization at the plasma membrane in cells growing in galactose or glucose as a sole carbon source (Tamayo Rojas et al., 2021b).
This study furthermore evaluated upstream signals caused by phosphorylation which triggers ubiquitination and consequent turnover of the targeted protein; using similar screening approaches to assess the stabilization of Gal2 by lysine residue modifications, it was possible to identify that N terminal serine residues 32, 35, 39, 48, 53, and 55 are likely involved in the internalization of Gal2, since a Gal2 construct where all these serines were mutated to alanine residues and tagged with GFP (Gal26SA_GFP) exhibited practically complete localization at the plasma membrane in cells growing in galactose or glucose as a sole carbon source (Tamayo Rojas et al., 2021b)...
Mutational analysis of ribosomal DNA and maturation-scheme analysis of ribosomal RNA in A. thaliana
(2022)
Ribosome biogenesis is a fundamental cellular process beginning with long precursor rRNA transcription from multi-copies of repetitive 45S ribosomal DNAs. At the subunit level, the primary pre-rRNA transcript encapsuled in 90S protein-RNA complex undergoes decisive splitting in two chief ways for further maturation into large (LSU) and small (SSU) ribosomal subunit. The usage of specific rDNA copies from defined chromosomes and their selective role during growth and development have been a topic of interest owing to its contribution to specialized ribosome theory which proposes non-monolithic functions for ribosomes and thereby their mRNA translation potential. Dual-guide CRISPR/Cas9 mediated disruption of rDNA regions resulted in stable disruption of up to 2.5% and 5% of all rDNA copies in hetero- and homozygous (ploop KD) conditions, respectively. At the RNA level, the mutation excised a critical structural element, P-loop on the LSU 25S rRNA. Mutation caused a dosage dependent defect with homozygosity leading to severe developmental defects through vegetative and reproductive growth phases which is manifested in their proteome by means of disregulation through both increase and decrease of several gene ontological categories of proteins in mutants. Interestingly, the mutation on chromosome 4 triggered dosage compensation through rRNA expression from chromosome 2 further compounded by ectopic rRNA biogenesis defects. The mutated copies however are not incorporated in the translating ribosomes and as a direct or indirect consequence led to elevated basal autophagic levels in the mutants.
The primary 35S transcript is known to undergo two modes of initial cleavages at the pre-rRNA level that aid in their subsequent maturation. Root cell culture (RCC) studies shows that these cells contain a novel ITS2-first cleaved precursor even under control growth conditions, P-C2 adding a third maturation means for the 35S pre-rRNA. This maturation path is further known to be triggered under elevated growth temperature forming a novel adaptive response in Arabidopsis and two other crop plants, tomato, and rice. Taken together, the pulse-chase labeling analysis of control and stressed tissues uncovers the fine-tuned pre-rRNA schematics with crossovers between multiple maturation paths.
Lipopolysaccharide (LPS) is a major glycolipid component in the outer leaflet of the outer membrane of Gram-negative bacteria and known as endotoxin exhibited by the lipid A moiety, which serves as a membrane anchor. The effective permeability barrier properties of the outer membrane contributed by the presence of LPS in the extracellular layer of the outer membrane confer Gram-negative bacteria a high resistance against hydrophobic compounds such as antibiotics, bile salts and detergents to survive in harsh environments. The biogenesis of LPS is well studied in Escherichia coli (herewith E. coli) and the LPS transport (Lpt) is carried out by a transenvelope complex composed of seven essential proteins (LptABCDEFG), which are located in the three compartments of the cell such as the outer membrane, the inner membrane and the periplasm. The Lpt system also exists in Anabaena sp. PCC 7120 (herewith Anabaena sp.), however, homologues of LptC and LptE are still missing. BLAST search failed to identify a homologue of LptC, in contrast, the secondary structure analysis using the Pfam database based on the existing ecLptC secondary structure identified one open reading frame All0231 as the putative Anabaena sp. homologue of LptC, which is designated anaLptC. Despite the low sequence similarity, the secondary structure alignment between anaLptC and ecLptC using the HHpred server showed that both proteins share high secondary structural similarities. The genotypic analysis of the insertion mutant anaLptC did not identify a fully segregated genome and its phenotypic analysis revealed that it was sensitive against chemicals, suggesting that the analptC gene is essential for the growth of Anabaena sp. and involved in the outer membrane biogenesis. This is further supported by the observation of the small cell phenotype in the anaLptC mutant via transmission electron microscopy. Moreover, physical interactions between the anaLptC periplasmic domain with anaLptA as well as with anaLptF were established, indicating that the anaLptC periplasmic domain is correctly folded and alone functional and that the transmembrane helix is not required for the interaction with anaLptA and anaLptF. Furthermore, the reduction of the O-antigen containing LPS was observed in the insertion mutant anaLptC and the dissociation constant Kd of the anaLptC periplasmic domain for ecLPS was determined.The three-dimensional structure of the periplasmic domain of anaLptC was solved by X-ray crystallography with a resolution of 2.8 Å. The structural superposition between the ecLptC crystal structure (PDB number 3my2) and the crystal structure of anaLptC periplasmic domain obtained by this study showed the similarity in the folding of the two proteins with a Cα r.m.s.d value of about 1 Å and confirmed that the length of anaLptC is more than two times longer than that of ecLptC. The structural comparison also revealed that both structures share the typical β-jellyroll fold and conserved amino acids, which were shown in ecLptC to bind to LPS in vivo and found in anaLptC. Overall, these data strongly suggest that anaLptC is involved in the transport of LPS and support the model whereby the bridge spanning the inner membrane and the outer membrane would be assembled via interactions of the structurally conserved β-jellyroll domains shared by five (LptACDFG) out of seven Lpt proteins.
In the framework of the PNRA (Italian National Antarctic Research Program) project CARBONANT focusing on biogenic carbonates and held in January–February 2002, several Ross Sea banks were sampled to obtain samples of biogenic carbonates. In the Mawson Bank, species belonging to the isopod genus Chaetarcturus Brandt, 1990 were recorded, including a specimen that did not match any described species. In this paper we describe Chaetarcturus cervicornis sp. n., which is characterized by supraocular spines and two pairs of tubercle-like protrusions on the cephalothorax. The new species is very similar to C. bovinus (Brandt & Wägele, 1988) and C. adareanus (Hodgson, 1902), but has a clearly different spine pattern. The study of the species of the genus Chaetarcturus in the Ross Sea contributes to increase our knowledge on the diversity of the Antarcturidae in the Southern Ocean. Ross Sea banks seem to hold an interesting and not-well-known fauna, deserving attention in future research.
Mitglieder der ubiquitär verbreiteten Cryptochrom-Photolyase-Familie sind Blaulicht-absorbierende Flavoproteine mit hoher Sequenzhomologie aber diversen Funktionen. Photolyasen katalysieren die Reparatur UV-Licht-induzierter DNA-Schäden. Cryptochrome (CRYs) wirken als lichtunabhängige Transkriptionsrepressoren innerhalb des Kern-Oszillators der circadianen Uhr oder als primäre Photorezeptoren zur Synchronisation dieser mit dem äußeren Tag-Nacht-Rhythmus und steuern durch Regulation der Genexpression Wachstum und Entwicklung. Gemeinsames Strukturmerkmal aller CPF-Vertreter ist die Photolyase- homologe Region (PHR), die das Chromophor Flavinadenindinukleotid (FAD) bindet, das lichtabhängig zwischen den Redoxformen oxidiert (FADox), semireduziert (FAD●- bzw. FADH●) und vollreduziert (FADH-) wechseln kann und damit die CRY-Konformation und -Aktivität beeinflusst. Unterscheidungsmerkmale sind die spezifische C-terminale Erweiterung (CTE) sowie die Komposition der FAD-Bindetasche, die unterschiedliche FAD-Redoxformen stabilisiert. Die Mechanismen der CRY-Photosignaltransduktion sind nicht völlig erforscht.
CryP ist eines von vier CRYs in der Diatomee Phaeodactylum tricornutum und gehört zur bislang nicht charakterisierten Gruppe pflanzenähnlicher CRYs. In vorhergehenden Untersuchungen wurde für CryP eine nukleare Lokalisation und damit verbunden eine blaulicht- sowie dunkelabhängige Regulation der Transkription unterschiedlichster Gene gezeigt. Zudem reguliert CryP das Proteinlevel photosynthetischer Lichtsammelkomplexe. CryP interagiert mit bisher nicht charakterisierten Proteinen aus dem Bereich DNA und Regulation sowie Ribosomen und Translation. Heterolog exprimiertes und isoliertes CryP stabilisiert das Neutralradikal FADH● und das Antennenchromophor Methenyltetrahydrofolat (MTHF).
In vorliegender Dissertation wurde die Bedeutung des FAD-Redoxzustands und der C-terminalen Proteindomäne für Strukturänderungen hinsichtlich der Oligomerisierung und Konformation sowie für das CryP-Interaktionsverhalten untersucht. Hierzu wurden rekombinante CryP-Varianten heterolog isoliert, die Mutationen in für die FAD-Reduzierbarkeit entscheidenden Aminosäuren oder eine Deletion der CTE tragen.
Die Analyse der CryP-Oligomerisierungsstufe und Konformation erfolgte mittels Ko-Präzipitation, nativen und zweidimensionalen PAGEs sowie partieller Proteolyse. Dabei wurde heterolog isoliertes CryP in seinen drei Redoxformen oxidiert (mit FADox), semireduziert (mit FADH●) und vollreduziert (mit FADH-) sowie das um die CTE-verkürzte CryP-PHR verglichen. Für CryP wurde eine redoxunabhängige, PHR-vermittelte Di- und Tetramerisierung über elektrostatische Wechselwirkung der Monomere beobachtet. Die CTE bindet spezifisch und redoxunabhängig an die PHR in einem Bereich um die FAD-Bindetasche. Dies schließt eine großräumige Konformationsänderung zwischen PHR und CTE infolge einer FAD-Photoreduktion wie für pflanzliche und viele tierische CRYs als Aktivierungsmechanismus für CryP aus.
Interaktionsstudien mittels zweidimensionaler PAGE gaben Aufschluss über unterschiedliche Bindeverhalten der beiden betrachteten Interaktionspartner an CryP. Sowohl BolA, ein potentieller redoxregulierter Transkriptionsfaktor, als auch ID42612 mit unbekannter Funktion interagieren mit CryP unabhängig von der FAD-Redoxform. Dabei bindet BolA an die CTE des CryP-Dimers und -Monomers, während ID42612 einen Komplex mit dem CryP-Dimer bildet.
Mittels in vitro Absorptions- und Fluoreszenzspektroskopie wurde die FAD-Redoxchemie von CryP und CryP-PHR verglichen. Die beiden Varianten unterscheiden sich in der FAD-Photoreduzierbarkeit und -Oxidationskinetik. Das Volllängenprotein CryP kann ohne externes Reduktionsmittel zum semireduzierten FADH● phototreduziert werden, das im Gegensatz zu bekannten CRYs über Tage im Dunkeln stabil gegen aerobe Oxidation ist. Eine Belichtung mit Reduktionsmittel führt zur Bildung des vollreduzierten FADH-, das innerhalb von Minuten zu FADH● rückoxidiert. Das um die CTE verkürzte CryP-PHR kann nur mit externem Reduktionsmittel zu FADH● photoreduziert werden, der vollreduzierte Zustand wird nie erreicht. Die Stabilisierung von FADH● gegen aerobe Oxidation im CryP-Holoprotein ist vergleichbar zur FAD-Redoxchemie von Photolyasen. Verglichen mit sonstigen charakterisierten CRYs ist die Wichtigkeit der CTE für eine effiziente FAD-Photoreduktion und FADH●-Stabilisierung eine CryP-spezifische Charakteristik.
Neben der CTE trägt die zu FAD-N5 proximal gelegene Position zur FADH●-Stabilisierung bei, wie Absorptionsmessungen an CryP_N417C zeigten. CryP weist mit Asparagin die gleiche Konservierung an dieser Position wie Photolyasen auf und unterscheidet sich damit ebenfalls von klassischen CRYs.
Analysen zur cryp-Transkription mittels qRT-PCR zeigten eine rhythmische Expression mit maximalen Transkriptmengen in der Nacht und eine rasche photoinduzierte Herunterregulation der Transkription...
Orientation hypercolumns in the visual cortex are delimited by the repeating pinwheel patterns of orientation selective neurons. We design a generative model for visual cortex maps that reproduces such orientation hypercolumns as well as ocular dominance maps while preserving retinotopy. The model uses a neural placement method based on t–distributed stochastic neighbour embedding (t–SNE) to create maps that order common features in the connectivity matrix of the circuit. We find that, in our model, hypercolumns generally appear with fixed cell numbers independently of the overall network size. These results would suggest that existing differences in absolute pinwheel densities are a consequence of variations in neuronal density. Indeed, available measurements in the visual cortex indicate that pinwheels consist of a constant number of ∼30, 000 neurons. Our model is able to reproduce a large number of characteristic properties known for visual cortex maps. We provide the corresponding software in our MAPStoolbox for Matlab.