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Unique features of a global human ectoparasite identified through sequencing of the bed bug genome
(2016)
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
Members of the Sm protein family are important for the cellular RNA metabolism in all three domains of life. The family includes archaeal and eukaryotic Lsm proteins, eukaryotic Sm proteins and archaeal and bacterial Hfq proteins. While several studies concerning the bacterial and eukaryotic family members have been published, little is known about the archaeal Lsm proteins. Although structures for several archaeal Lsm proteins have been solved already more than ten years ago, we still do not know much about their biological function, however one can confidently propose that the archaeal Lsm proteins will also be involved in RNA metabolism. Therefore, we investigated this protein in the halophilic archaeon Haloferax volcanii. The Haloferax genome encodes a single Lsm protein, the lsm gene overlaps and is co-transcribed with the gene for the ribosomal L37.eR protein. Here, we show that the reading frame of the lsm gene contains a promoter which regulates expression of the overlapping rpl37R gene. This rpl37R specific promoter ensures high expression of the rpl37R gene in exponential growth phase. To investigate the biological function of the Lsm protein we generated a lsm deletion mutant that had the coding sequence for the Sm1 motif removed but still contained the internal promoter for the downstream rpl37R gene. The transcriptome of this deletion mutant was compared to the wild type transcriptome, revealing that several genes are down-regulated and many genes are up-regulated in the deletion strain. Northern blot analyses confirmed down-regulation of two genes. In addition, the deletion strain showed a gain of function in swarming, in congruence with the up-regulation of transcripts encoding proteins required for motility.
Zinc finger domains are highly structured and can mediate interactions to DNA, RNA, proteins, lipids, and small molecules. Accordingly, zinc finger proteins are very versatile and involved in many biological functions. Eukaryotes contain a wealth of zinc finger proteins, but zinc finger proteins have also been found in archaea and bacteria. Large zinc finger proteins have been well studied, however, in stark contrast, single domain zinc finger µ-proteins of less than 70 amino acids have not been studied at all, with one single exception. Therefore, 16 zinc finger µ-proteins of the haloarchaeon Haloferax volcanii were chosen and in frame deletion mutants of the cognate genes were generated. The phenotypes of mutants and wild-type were compared under eight different conditions, which were chosen to represent various pathways and involve many genes. None of the mutants differed from the wild-type under optimal or near-optimal conditions. However, 12 of the 16 mutants exhibited a phenotypic difference under at least one of the four following conditions: Growth in synthetic medium with glycerol, growth in the presence of bile acids, biofilm formation, and swarming. In total, 16 loss of function and 11 gain of function phenotypes were observed. Five mutants indicated counter-regulation of a sessile versus a motile life style in H. volcanii. In conclusion, the generation and analysis of a set of deletion mutants demonstrated the high importance of zinc finger µ-proteins for various biological functions, and it will be the basis for future mechanistic insight.
Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.
BACKGROUND: Attention-Deficit/Hyperactivity Disorder (ADHD) is one of the most common neurodevelopmental disorders worldwide. As described in the DSM-5, ADHD is clinically heterogeneous with three main subtypes; predominant hyperactive, predominant attention deficit and combined. The severity of symptoms widely differs among the patients and interferes with the person functioning, negatively impacting social and occupational activities (American Psychiatric Association, 2013). Despite the many efforts, the etiology of the disorder is still unclear. Therefore, there is an increasing demand of models that would help elucidating the causative mechanisms of the disorder and, in parallel, would be valuable tools to discover new and effective treatments. The main goal of the study is the identification of disease specific cellular phenotypes related to Attention-Deficit/Hyperactivity Disorder (ADHD) in cellular models from patients carrying rare copy number variants (CNVs) in the PARK2 locus that have been previously associated with ADHD (Elia et al., 2010; Jarick et al., 2014).
METHODS: Human dermal fibroblast (HDF) cultures were obtained from skin punches and reprogrammed into human induced pluripotent stem cells (HiPSC) and successively induced to differentiate into HiPSC-derived dopaminergic neurons. Both HiPSC and HiPSC-derived neurons, were proven to be bona fide models by morphological analysis, RT-PCR, RT-qPCR, immunofluorescence, embryoid body assay, molecular karyotyping and dopamine level quantification. A total of six donors were selected for HiPSC and dopaminergic neuron generation: 3 adult ADHD PARK2 CNV risk carriers (1 duplication and 2 deletion carriers, 1 ADHD non-risk CNV variant carrier and 2 healthy controls).
We conducted stress-response experiments (nutrient deprivation and CCCP administration) that are well known to increase PARK2 expression, on both fibroblasts and HiPSC. After assessing PARK2 gene and protein expression levels, we evaluated the gene expression of genes that are involved with different processes orchestrated by PARK2. We then performed a series of assays with a special focus on mitochondrial function and energy metabolism (ATP production, basal oxygen consumption rates, ROS abundance) and evaluated changing in the mitochondrial network morphology.
To evaluate the effect of nicotine exposure, one of the best replicated prenatal risk factors for having a child later on diagnosed with ADHD, we treated HiPSC-derived dopaminergic neurons with smoking-relevant nicotine concentrations and evaluated PARK2 protein expression after treatment and gene expression by RNA sequencing.
RESULTS: The cell models created in this study passed all the characterization tests required to assess whether the lines can be considered bona fide models without underling genotype differences. The evaluation of patho-phenotypes connected with ADHD/PARK2 CNVs in HDF and HIPSC showed that, although PARK2 gene expression was unchanged, ADHD/PARK2 CNV carriers show different PARK2 protein levels possibly implying the presence of different post-transcriptional processes. ADHD/PARK2 CNV carriers show lower levels of ATP production and basal oxygen consumption rates compared to controls, a result in line with what was already reported in ADHD cybrids cells model (Verma et al., 2016). Our experiments indicate that both the amount of reactive oxygen species (ROS) and the mitochondrial network morphology is influenced by the treatment but not by the genotype. The evaluation of nicotine effects on HiPSC-derived dopaminergic neuron from aADHD patients showed no effects on PARK2 protein levels and gene expression. ADHD/PARK2 CNVs carriers show gene ontology enrichment in modules connected with the regulation of cell growth after nicotine acute treatment. Additionally, genes connected with energy production & oxidative stress response and extracellular matrix & cell adhesion were significantly differentially expressed after nicotine treatments.
CONCLUSIONS: This study points out the presence of impairment of mitochondrial energetics in cellular models derived from adult ADHD patients carrying rare CNVs within the PARK2 locus. In the last years, several studies have linked mitochondrial impairments to the etiology of psychiatric and neurodevelopmental disorders (McCann & Ross, 2018) and reported an overall increase of oxidative stress or insufficient response to oxidative damage both in children and adults with ADHD (Joseph, Zhang-James, Perl, & Faraone, 2015; Lopresti, 2015). Additionally, different groups have underlined an abnormal brain connectivity in ADHD patients in their work (Gehricke et al., 2017). Our preliminary investigation of the effects of a well-known prenatal risk factor for ADHD, nicotine gestation exposure, point out a susceptibility of the PARK2 CNVs carriers in processes involved in regulation of cell growth and in proteins connected with extracellular matrix composition and cell-adhesion molecules, all factors necessary for neuronal maturation and formation of proper neural connections (Washbourne et al., 2004). In conclusion, this study presents novel and fully validated cellular model systems to study the etiopathogenesis of ADHD based on rare CNVs in the PARK2 locus. Moreover, the identification of disease-relevant phenotypes in the model might be helpful in the future for testing new alternative medications.
Drebrin (DBN) regulates cytoskeletal functions during neuronal development, and is thought to contribute to structural and functional synaptic changes associated with aging and Alzheimer’s disease. Here we show that DBN coordinates stress signalling with cytoskeletal dynamics, via a mechanism involving kinase ataxia-telangiectasia mutated (ATM). An excess of reactive oxygen species (ROS) stimulates ATM-dependent phosphorylation of DBN at serine-647, which enhances protein stability and accounts for improved stress resilience in dendritic spines. We generated a humanized DBN Caenorhabditis elegans model and show that a phospho-DBN mutant disrupts the protective ATM effect on lifespan under sustained oxidative stress. Our data indicate a master regulatory function of ATM-DBN in integrating cytosolic stress-induced signalling with the dynamics of actin remodelling to provide protection from synapse dysfunction and ROS-triggered reduced lifespan. They further suggest that DBN protein abundance governs actin filament stability to contribute to the consequences of oxidative stress in physiological and pathological conditions.
Die Analyse von DNA-Sequenzen steht spätestens seit der Feststellung ihrer tragenden Rolle in der Vererbung organismischer Eigenschaften im Fokus biologischer Fragestellungen. Seit Kurzem wird mit modernsten Methoden die Untersuchung von kompletten Genomen ermöglicht. Dies eröffnet den Zugang zu genomweiten Informationen gegenüber begrenzt aussagekräftigen markerbasierten Analysen. Eine Genomsequenz ist die ultimative Quelle an organismischer Information. Allerdings sind diese Informationen oft aufgrund technischer und biologischer Gründe komplex und werfen meist mehr Fragen auf, als sie beantworten.
Die Rekonstruktion einer bislang unbekannten Genomsequenz aus kurzen Sequenzen stellt eine technische Herausforderung dar, die mit grundlegenden, aber in der Realität nicht zwingend zutreffenden Annahmen verbunden ist. Außerdem können biologische Faktoren, wie Repeatgehalt oder Heterozygotie, die Fehlerrate einer Assemblierung stark beeinflussen. Die Beurteilung der Qualität einer de novo Assemblierung ist herausfordernd, aber zugleich äußerst notwendig. Anschließend ist eine strukturelle und funktionale Annotation von Genen, kodierenden Bereichen und repeats nötig, um umfangreiche biologische Fragestellungen beantworten zu können. Ein qualitativ hochwertiges und annotiertes assembly ermöglicht genomweite Analysen von Individuen und Populationen. Diese Arbeit beinhaltet die Assemblierung und Annotation des Genoms der Süßwasserschnecke Radix auricularia und eine Studie vergleichender Genomik von fünf Individuen aus verschiedenen molekularen Gruppen (MOTUs).
Mollusken beherbergen nach den Insekten die größte Artenvielfalt innerhalb der Tierstämme und besiedeln verschiedenste, teils extreme, Habitate. Trotz der großen Bedeutung für die Biodiversitätsforschung sind verhältnismäßig wenige genomische Daten öffentlich verfügbar. Zudem sind Arten der Gattung Radix auch aufgrund ihrer großen geografischen Verbreitung in diversen biologischen Disziplinen als Modellorganismen etabliert. Eine annotierte Genomsequenz ermöglicht über bereits untersuchte Felder hinaus die Forschung an grundlegenden biologischen Fragestellungen, wie z.B. die Funktionsweise von Hybridisierung und Artbildung. Durch Assemblierung und scaffolding von sechs whole genome shotgun Bibliotheken verschiedener insert sizes und einem transkriptbasiertem scaffolding konnte trotz des hohen Repeatgehalts ein vergleichsweise kontinuierliches assembly erhalten werden. Die erhebliche Differenz zwischen der Gesamtlänge der Assemblierung und der geschätzten Genomgröße konnte zum Großteil auf kollabierte repeats zurückgeführt werden.
Die strukturelle Annotation basierend auf Transkriptomen, Proteinen einer Datenbank und artspezifisch trainierten Genvorhersagemodellen resultierte in 17.338 proteinkodierenden Genen, die etwa 12,5% der geschätzten Genomgröße abdecken. Der Annotation wird u.a. aufgrund beinhaltender Kernrthologen, konservierter Proteindomänenarrangements und der Übereinstimmung mit de novo sequenzierten Peptiden eine hohe Qualität zugesprochen.
Das mapping der Sequenzen von fünf Radix MOTUs gegen die R. auricularia Assemblierung zeigte stark verringerte coverage außerhalb kodierender Bereiche der nicht-Referenz MOTUs aufgrund hoher Nukleotiddiversität. Für 16.039 Gene konnten Topologien berechnet werden und ein Test auf positive Selektion ausgeführt werden. Insgesamt konnte über alle MOTUs hinweg in 678 verschiedenen Genen positive Selektion detektiert werden, wobei jede MOTU ein nahezu einzigartiges Set positiv selektierter Gene beinhaltet. Von allen 16.039 untersuchten Genen konnten 56,4% funktional annotiert werden. Diese niedrige Rate wird vermutlich durch Mangel an genomischer Information in Mollusken verursacht. Anschließende Analysen auf Anreicherungen von Funktionen sind deshalb nur bedingt repräsentativ.
Neben den biologischen Ergebnissen wurden Methoden und Optimierungen genomischer Analysen von Nichtmodellorganismen entwickelt. Dazu zählen eigens angefertigte Skripte, um beispielsweise Transkriptomalignments zu filtern, Trainings eines Genvorhersagemodells automatisiert und parallelisiert auszuführen und Orthogruppen bestimmter Arten aus einer Orthologievorhersage zu extrahieren. Zusätzlich wurden Abläufe entwickelt, um möglichst viele vorhandene Daten in die Assemblierung und Annotation zu integrieren. Etwa wurde ein zusätzliches scaffolding mit eigens assemblierten Transkripten mehrerer MOTUs sequenziell und phylogenetisch begründet ausgeführt.
Insgesamt wird eine umfassende und qualitativ hochwertige Genomsequenz eines Süßwassermollusken präsentiert, welche eine Grundlage für zukünftige Forschungsprojekte z.B. im Bereich der Biodiversität, Populationsgenomik und molekularen Ökologie bietet. Die Ergebnisse dieser Arbeit stellen einen Wissenszuwachs in der Genomik von Mollusken dar, welche bisher trotz ihrer Artenvielfalt deutlich unterrepräsentiert bezüglich assemblierter und annotierter Genome auffallen.
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N2 fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O2 evolution and CO2 fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N2 fixation, H2 metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (−750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
Haloferax volcanii is a well-established model species for haloarchaea. Small scale RNomics and bioinformatics predictions were used to identify small non-coding RNAs (sRNAs), and deletion mutants revealed that sRNAs have important regulatory functions. A recent dRNA-Seq study was used to characterize the primary transcriptome. Unexpectedly, it was revealed that, under optimal conditions, H. volcanii contains more non-coding sRNAs than protein-encoding mRNAs. However, the dRNA-Seq approach did not contain any length information. Therefore, a mixed RNA-Seq approach was used to determine transcript length and to identify additional transcripts, which are not present under optimal conditions. In total, 50 million paired end reads of 150 nt length were obtained. 1861 protein-coding RNAs (cdRNAs) were detected, which encoded 3092 proteins. This nearly doubled the coverage of cdRNAs, compared to the previous dRNA-Seq study. About 2/3 of the cdRNAs were monocistronic, and 1/3 covered more than one gene. In addition, 1635 non-coding sRNAs were identified. The highest fraction of non-coding RNAs were cis antisense RNAs (asRNAs). Analysis of the length distribution revealed that sRNAs have a median length of about 150 nt. Based on the RNA-Seq and dRNA-Seq results, genes were chosen to exemplify characteristics of the H. volcanii transcriptome by Northern blot analyses, e.g. 1) the transcript patterns of gene clusters can be straightforward, but also very complex, 2) many transcripts differ in expression level under the four analyzed conditions, 3) some genes are transcribed into RNA isoforms of different length, which can be differentially regulated, 4) transcripts with very long 5’-UTRs and with very long 3’-UTRs exist, and 5) about 30% of all cdRNAs have overlapping 3’-ends, which indicates, together with the asRNAs, that H. volcanii makes ample use of sense-antisense interactions. Taken together, this RNA-Seq study, together with a previous dRNA-Seq study, enabled an unprecedented view on the H. volcanii transcriptome.