Molekulare Charakterisierung des NOD-like Rezeptors NLRC5

NOD-like Rezeptoren (NLR) repräsentieren eine Gruppe von intrazellulären Sensor-Proteinen des angeborenen Immunsystems, die pathogen-assoziierte Moleküle (PAMPs) oder andere zytosolische Gefahrensignale (DAMPs) erkennen. Ihre essentielle Rolle für die Verteidigung gegen Pathogene wird dadurch unterstrichen, dass Mutationen in den NLR-Genen mit einer großen Bandbreite von entzündlichen Krankheiten assoziiert wurden. In der vorliegenden Arbeit wurde die genomische Organisation, die Regulation und Funktionsweise des NLR-Familienmitglieds NLRC5 untersucht. Die Ergebnisse zeigen, dass NLRC5 an antiviralen Signalprozessen beteiligt ist. Nach einer viralen Infektion kommt es zu einer erhöhten Expression von IFN-, was durch autokrine Mechanismen zu einer erhöhten Expression von NLRC5 führt. An dieser transkriptionellen Kontrolle sind Komponenten der gamma-interferon activation sequence (GAS) Signalkaskaden beteiligt. Künstlich aktiviertes NLRC5 bewirkt die Aktivierung von zwei bisher nicht mit NLR-Proteinen assoziierten Signalwegen. Die Aktivierung von interferon-specific response element (ISRE)- und GAS- Promotorelementen führt zu einer gesteigerten Expression von antiviralen Zielgenen (IFN-, OAS1, PRKRIR). Zusätzlich führte Überexpression oder künstliche Oligomerisierung von NLRC5 zu einer verstärkten und über einen längeren Zeitraum andauernden Phosphorylierung des Transkriptionsfaktors STAT1, der an der Vermittlung von antiviralen Prozessen beteiligt ist. Die Ergebnisse deuten darauf hin, dass NLRC5 einen wichtigen molekularen Schalter des GAS/ISRE-Signalwegs repräsentiert, der dazu beiträgt, antivirale Verteidigungsmechnismen zu aktivieren. Die Ergebnisse dieser Arbeit zeigen zusätzlich eine bisher nicht beschriebene Interaktion zwischen zwei NLR-Mitgliedern. Durch homophile NACHT-NACHT – Interaktion zwischen NLRC5 und NOD2 kommt es zu einer verstärkten NOD2-abhängigen NF-B- und NLRC5-vermittelten ISRE-Aktivierung. Koexpression beider Proteine vermittelt außerdem einen erhöhten Schutz gegen bakterielle Zytoinvasion im Listeria monocytogenes – Infektionsmodell. Die Ergebnisse dieser Arbeit deuten darauf hin, dass die protektiven Eigenschaften von NLR-Proteinen innerhalb des angeborenen Immunsystem und die damit verbundenen aktivierten Signalkaskaden weit vielfältiger sind als bisher angenommen. Die Interaktion zwischen den verschiedenen NLR-Familienmitgliedern scheint dabei ein nicht zu unterschätzender Faktor zu sein, der in Zukunft stärker beachtet werden sollte.NOD-like receptors (NLRs) represent a group of intracellular proteins of the innate immune system which recognize pathogen-associated molecular patterns (PAMPs) or other cytosolic danger signals (DAMPs). Mutations in NLR genes have been linked to a variety of inflammatory diseases underscoring their pivotal role in host defense and immunity. This work describes the genomic organisation and regulation of the human NLR-family member NLRC5. The results show that NLRC5 is involved in antiviral signal processes. Viral infection induced an increased expression of IFN-, and led through an autocrine mechanism, to an enhanced expression of NLRC5. The transcription is regulated by components of the gamma-interferon activation sequence (GAS) cascade. Artificial oligomerisation of NLRC5 lead to an activation of two new signal transduction pathways, which were until now not associated with NLR proteins. The activation of interferon-specific response element (ISRE)- and GAS-promotor elements resulted in an enhanced expression of antiviral target genes (IFN-, OAS1, PRKRIR). Additionally, overexpression or enforced oligomerisation of NLRC5 led to an increase in phosphorylation of the transcription factor STAT1, which is involved in antiviral processes. The results indicate that NLRC5 represents an important molecular regulator for the GAS/ISRE-pathway and helps to activate antiviral defense programms. Furthermore, the results show a new interaction between two members of the NLR-family. The homophilia NACHT-NACHT – interaction between NLRC5 and NOD2 induce an increased NOD2-dependent NF-B- and NLRC5-mediated ISRE-activation. Co-expression of both proteins mediated an increased protection against the cytoinvasive bacteria Listeria monocytogenes. The results suggest that the protective properties of NLR-proteins for the innate immunity with the associated signal cascades are multifaceted. They also underpin the importance of understanding the interactions between different NLR-family members in immune response to infections and highlight the need in future investigations

Draft Genome Sequence of Ideonella sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm

Here, we report the draft genome sequence of the betaproteobacterium Ideonella sp. strain A_228. This isolate, obtained from a bog iron ore-containing floodplain area in Germany, provides valuable information about the genetic diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq technique was used to sequence the draft genome sequence of the strain.BMBF, 02WU0715, Verbundprojekt: Entwicklung eines Indikatorsystems für Verockerungsprozesse - Teilprojekt 1: Untersuchung der Biofilme der Oder-Auen: Diversität und umweltbiotechnologisches Potenzial; Teilprojekt 3: Klärung des Abbaus persistenter organischer Schadstoffe bei mikrobiellen Prozesse

Draft Genome Sequence of the Gram-Positive Neutrophilic Iron-Precipitating Kineosporia sp. Strain A_224

We report here the draft genome sequence of the neutrophilic iron-precipitating Kineosporia sp. strain A_224. Analysis of the predicted genes may improve our knowledge of its role in ochrous formations in natural and technical water systems. This is the first public genome sequence of a Kineosporia aurantiaca strain.BMBF, 02WU0715, Verbundprojekt: Entwicklung eines Indikatorsystems für Verockerungsprozesse - Teilprojekt 1: Untersuchung der Biofilme der Oder-Auen: Diversität und umweltbiotechnologisches Potenzial; Teilprojekt 3: Klärung des Abbaus persistenter organischer Schadstoffe bei mikrobiellen Prozesse

Draft genome sequence of strain B 225, an iron-depositing isolate of the genus Novosphingobium

Here, we report the draft genome sequence of Novosphingobium sp. strain B 225, an iron-depositing bacterium isolated from a phenazone-amended naturally grown biofilm. This biofilm was grown in the Unteres Odertal National Park, Germany. Illumina NextSeq sequencing was used to determine the genome of the strain.DFG, 325093850, Open Access Publizieren 2017 - 2018 / Technische Universität Berli

Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins

Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria employing this photosystem in nature. Almost complete pufLM gene sequences and the derived protein sequences from 152 type strains and 45 additional strains of phototrophic Proteobacteria employing photosystem II were compared. The results give interesting and comprehensive insights into the phylogeny of the photosynthetic apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from Caulobacterales (Brevundimonas subvibrioides). A special relationship exists between the PufLM sequences of those bacteria employing bacteriochlorophyll b instead of bacteriochlorophyll a. A clear phylogenetic association of aerobic phototrophic purple bacteria to anaerobic purple bacteria according to their PufLM sequences is demonstrated indicating multiple evolutionary lines from anaerobic to aerobic phototrophic purple bacteria. The impact of pufLM gene sequences for studies on the environmental diversity of phototrophic bacteria is discussed and the possibility of their identification on the species level in environmental samples is pointed out. © 2018 Imhoff, Rahn, Künzel and Neulinger

Evaluating the Impact of Wastewater Effluent on Microbial Communities in the Panke, an Urban River

Pharmaceuticals are consumed in high amounts and can enter as emerging organic compounds in surface waters as they are only partially retained in wastewater treatment plants (WWTPs). Receiving pharmaceuticals may burden the aquatic environment, as they are designed to be bioactive even at low concentrations. Sediment biofilm populations were analyzed in river sediments due to the exposure of an inflow of WWTP effluents. Illumina MiSeq 16S rRNA gene amplicon sequencing was performed of 108 sediment samples, which were taken from multiple cores within three sampling locations in the Panke River, with one sampling site located downstream of the inflow. Sequencing data were processed to infer microbial community structure in samples concerning the environmental variables, such as micropollutants and physicochemical parameters measured for each core. More than 25 different micropollutants were measured in pore water samples, in which bezafibrate, clofibric acid, carbamazepine, and diclofenac were detected at high concentrations. Bacterial 16S rRNA gene amplicons revealed Nitrospirae, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Bacteroidetes, and Ignavibacteriae as the most abundant groups in the samples. Differences in microbial community composition were observed with respect to micropollutants. However, our findings revealed that the composition of the microbial community was not only governed by the effluent. The significant changes in the alpha- and beta-diversity were explained by phenobarbital and SO42−, which did not originate from the WWTP indicating that more unobserved factors are also likely to play a role in affecting the biofilm community’s composition.DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität BerlinDFG, 248198858, GRK 2032: Grenzzonen in urbanen Wassersysteme

Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability

Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10–11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in situ) and pCO2 (adjusted to ∼1100 μatm) were tested for their single and combined effects on epibacterial communities of the brown macroalga Fucus vesiculosus and on bacteria present in the surrounding seawater. The experiments were set up in three biological replicates using the Kiel Outdoor Benthocosm facility (Kiel, Germany). Phylogenetic analyses of the respective microbiota were performed by bacterial 16S (V1-V2) rDNA Illumina MiSeq amplicon sequencing after 0, 4, 8, and 10/11 weeks per season. The results demonstrate (I) that the bacterial community composition varied in time and (II) that relationships between operational taxonomic units (OTUs) within an OTU association network were mainly governed by the habitat. (III) Neither single pCO2 nor pCO2:Temperature interaction effects were statistically significant. However, significant impact of ocean warming was detected varying among seasons. (IV) An indicator OTU (iOTU) analysis identified several iOTUs that were strongly influenced by temperature in spring, summer, and winter. In the warming treatments of these three seasons, we observed decreasing numbers of bacteria that are commonly associated with a healthy marine microbial community and—particularly during spring and summer—an increase in potentially pathogenic and bacteria related to intensified microfouling. This might lead to severe consequences for the F. vesiculosus holobiont finally affecting the marine ecosystem

Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses

Osmotic adaptation and accumulation of compatible solutes is a key process for life at high osmotic pressure and elevated salt concentrations. Most important solutes that can protect cell structures and metabolic processes at high salt concentrations are glycine betaine and ectoine. The genome analysis of more than 130 phototrophic bacteria shows that biosynthesis of glycine betaine is common among marine and halophilic phototrophic Proteobacteria and their chemotrophic relatives, as well as in representatives of Pirellulaceae and Actinobacteria, but are also found in halophilic Cyanobacteria and Chloroherpeton thalassium. This ability correlates well with the successful toleration of extreme salt concentrations. Freshwater bacteria in general lack the possibilities to synthesize and often also to take up these compounds. The biosynthesis of ectoine is found in the phylogenetic lines of phototrophic Alpha- and Gammaproteobacteria, most prominent in the Halorhodospira species and a number of Rhodobacteraceae. It is also common among Streptomycetes and Bacilli. The phylogeny of glycine-sarcosine methyltransferase (GMT) and diaminobutyrate-pyruvate aminotransferase (EctB) sequences correlate well with otherwise established phylogenetic groups. Most significantly, GMT sequences of cyanobacteria form two major phylogenetic branches and the branch of Halorhodospira species is distinct from all other Ectothiorhodospiraceae. A variety of transport systems for osmolytes are present in the studied bacteri

Draft genome sequence of actinobacterial strain Kineosporia sp. R_H_3, a neutrophilic iron-depositing bacterium

The draft genome sequence of a neutrophilic iron-depositing actinobacterial strain, Kineosporia sp. R_H_3, is reported here. Detailed analysis of the genome can elucidate the role of specific cytochromes for Fe oxidation and how this organism might receive energy from Fe oxidation. To date, this is the second publicly available genome sequence of a Kineosporia strain.DFG, 325093850, Open Access Publizieren 2017 - 2018 / Technische Universität Berli

Effects of a male meiotic driver on male and female transcriptomes in the house mouse

Not all genetic loci follow Mendel's rules, and the evolutionary consequences of this are not yet fully known. Genomic conflict involving multiple loci is a likely outcome, as restoration of Mendelian inheritance patterns will be selected for, and sexual conflict may also arise when sexes are differentially affected. Here, we investigate effects of the t haplotype, an autosomal male meiotic driver in house mice, on genome-wide gene expression patterns in males and females. We analysed gonads, liver and brain in adult same-sex sibling pairs differing in genotype, allowing us to identify t-associated differences in gene regulation. In testes, only 40% of differentially expressed genes mapped to the approximately 708 annotated genes comprising the t haplotype. Thus, much of the activity of the t haplotype occurs in trans, and as upregulation. Sperm maturation functions were enriched among both cis and trans acting t haplotype genes. Within the t haplotype, we observed more downregulation and differential exon usage. In ovaries, liver and brain, the majority of expression differences mapped to the t haplotype, and were largely independent of the differences seen in the testis. Overall, we found widespread transcriptional effects of this male meiotic driver in the house mouse genome