Flavofun: Exploration of fungal flavoproteomes

Fungi produce a plethora of natural products exhibiting a fascinating diversity of chemical structures with an enormous potential for medical applications. Despite the importance of understanding the scope of natural products and their biosynthetic pathways, a systematic analysis of the involved enzymes has not been undertaken. In our previous studies, we examined the flavoprotein encoding gene pool in archaea, eubacteria, the yeast Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. In the present survey, we have selected the model fungus Neurospora crassa as a starting point to investigate the flavoproteomes in the fungal kingdom. Our analysis showed that N. crassa harbors 201 flavoprotein-encoding genes amounting to 2% of the total protein-encoding genome. The majority of these flavoproteins (133) could be assigned to primary metabolism, termed the “core flavoproteome”, with the remainder of flavoproteins (68) serving in, as yet unidentified, reactions. The latter group of “accessory flavoproteins” is dominated by monooxygenases, berberine bridge enzyme-like enzymes, and glucose-methanol-choline-oxidoreductases. Although the exact biochemical role of most of these enzymes remains undetermined, we propose that they are involved in activities closely associated with fungi, such as the degradation of lignocellulose, the biosynthesis of natural products, and the detoxification of harmful compounds in the environment. Based on this assumption, we have analyzed the accessory flavoproteomes in the fungal kingdom using the MycoCosm database. This revealed large differences among fungal divisions, with Ascomycota, Basidiomycota, and Mucoromycota featuring the highest average number of genes encoding accessory flavoproteins. Moreover, a more detailed analysis showed a massive accumulation of accessory flavoproteins in Sordariomycetes, Agaricomycetes, and Glomeromycotina. In our view, this indicates that these fungal classes are proliferative producers of natural products and also interesting sources for flavoproteins with potentially useful catalytic properties in biocatalytic applications

DataSheet1_Flavofun: Exploration of fungal flavoproteomes.docx

Fungi produce a plethora of natural products exhibiting a fascinating diversity of chemical structures with an enormous potential for medical applications. Despite the importance of understanding the scope of natural products and their biosynthetic pathways, a systematic analysis of the involved enzymes has not been undertaken. In our previous studies, we examined the flavoprotein encoding gene pool in archaea, eubacteria, the yeast Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. In the present survey, we have selected the model fungus Neurospora crassa as a starting point to investigate the flavoproteomes in the fungal kingdom. Our analysis showed that N. crassa harbors 201 flavoprotein-encoding genes amounting to 2% of the total protein-encoding genome. The majority of these flavoproteins (133) could be assigned to primary metabolism, termed the “core flavoproteome”, with the remainder of flavoproteins (68) serving in, as yet unidentified, reactions. The latter group of “accessory flavoproteins” is dominated by monooxygenases, berberine bridge enzyme-like enzymes, and glucose-methanol-choline-oxidoreductases. Although the exact biochemical role of most of these enzymes remains undetermined, we propose that they are involved in activities closely associated with fungi, such as the degradation of lignocellulose, the biosynthesis of natural products, and the detoxification of harmful compounds in the environment. Based on this assumption, we have analyzed the accessory flavoproteomes in the fungal kingdom using the MycoCosm database. This revealed large differences among fungal divisions, with Ascomycota, Basidiomycota, and Mucoromycota featuring the highest average number of genes encoding accessory flavoproteins. Moreover, a more detailed analysis showed a massive accumulation of accessory flavoproteins in Sordariomycetes, Agaricomycetes, and Glomeromycotina. In our view, this indicates that these fungal classes are proliferative producers of natural products and also interesting sources for flavoproteins with potentially useful catalytic properties in biocatalytic applications.</p

DataSheet2_Flavofun: Exploration of fungal flavoproteomes.docx

Fungi produce a plethora of natural products exhibiting a fascinating diversity of chemical structures with an enormous potential for medical applications. Despite the importance of understanding the scope of natural products and their biosynthetic pathways, a systematic analysis of the involved enzymes has not been undertaken. In our previous studies, we examined the flavoprotein encoding gene pool in archaea, eubacteria, the yeast Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. In the present survey, we have selected the model fungus Neurospora crassa as a starting point to investigate the flavoproteomes in the fungal kingdom. Our analysis showed that N. crassa harbors 201 flavoprotein-encoding genes amounting to 2% of the total protein-encoding genome. The majority of these flavoproteins (133) could be assigned to primary metabolism, termed the “core flavoproteome”, with the remainder of flavoproteins (68) serving in, as yet unidentified, reactions. The latter group of “accessory flavoproteins” is dominated by monooxygenases, berberine bridge enzyme-like enzymes, and glucose-methanol-choline-oxidoreductases. Although the exact biochemical role of most of these enzymes remains undetermined, we propose that they are involved in activities closely associated with fungi, such as the degradation of lignocellulose, the biosynthesis of natural products, and the detoxification of harmful compounds in the environment. Based on this assumption, we have analyzed the accessory flavoproteomes in the fungal kingdom using the MycoCosm database. This revealed large differences among fungal divisions, with Ascomycota, Basidiomycota, and Mucoromycota featuring the highest average number of genes encoding accessory flavoproteins. Moreover, a more detailed analysis showed a massive accumulation of accessory flavoproteins in Sordariomycetes, Agaricomycetes, and Glomeromycotina. In our view, this indicates that these fungal classes are proliferative producers of natural products and also interesting sources for flavoproteins with potentially useful catalytic properties in biocatalytic applications.</p

The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Eggers, Reinmar, Jammer, Alexandra, Jha, Shalinee, Kerschbaumer, Bianca, Lahham, Majd, Strandback, Emilia, Toplak, Marina, Wallner, Silvia, Winkler, Andreas, Macheroux, Peter (2021): The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana. Phytochemistry (112822) 189: 1-42, DOI: 10.1016/j.phytochem.2021.112822, URL: http://dx.doi.org/10.1016/j.phytochem.2021.11282

Phosphorylation of different tau sites during progression of Alzheimer’s disease

Abstract Alzheimer’s disease is characterized by accumulation of amyloid plaques and tau aggregates in several cortical brain regions. Tau phosphorylation causes formation of neurofibrillary tangles and neuropil threads. Phosphorylation at tau Ser202/Thr205 is well characterized since labeling of this site is used to assign Braak stage based on occurrence of neurofibrillary tangles. Only little is known about the spatial and temporal phosphorylation profile of other phosphorylated tau (ptau) sites. Here, we investigate total tau and ptau at residues Tyr18, Ser199, Ser202/Thr205, Thr231, Ser262, Ser396, Ser422 as well as amyloid-β plaques in human brain tissue of AD patients and controls. Allo- and isocortical brain regions were evaluated applying rater-independent automated quantification based on digital image analysis. We found that the level of ptau at several residues, like Ser199, Ser202/Thr205, and Ser422 was similar in healthy controls and Braak stages I to IV but was increased in Braak stage V/VI throughout the entire isocortex and transentorhinal cortex. Quantification of ThioS-stained plaques showed a similar pattern. Only tau phosphorylation at Tyr18 and Thr231 was already significantly increased in the transentorhinal region at Braak stage III/IV and hence showed a progressive increase with increasing Braak stages. Additionally, the increase in phosphorylation relative to controls was highest at Tyr18, Thr231 and Ser199. By contrast, Ser396 tau and Ser262 tau showed only a weak phosphorylation in all analyzed brain regions and only minor progression. Our results suggest that the ptau burden in the isocortex is comparable between all analyzed ptau sites when using a quantitative approach while levels of ptau at Tyr18 or Thr231 in the transentorhinal region are different between all Braak stages. Hence these sites could be crucial in the pathogenesis of AD already at early stages and therefore represent putative novel therapeutic targets

Additional file 1: of Phosphorylation of different tau sites during progression of Alzheimer’s disease

Online Source 9 Double labeling of pSer262 and pSer202/Thr205 tau in the temporal cortex at Braak stage V/VI. Images show different labeling pattern of pSer262 (arrows) and pS202 (white arrowheads) as well as their overlay (yellow arrowheads) (a1) and single fluorescence images (a2,3,4) of case 17. AF: autofluorescence. Scale bar: 20 μm. Online Source 10 Example of measurement procedure of tau pSer262. Objects in the unlabeled autofluorescence channel were detected by thresholding (red in a1). The resulting mask images (a2) were then subtracted from tau pSer262 images to remove autofluorescence (a3). The resulting images were Edge+ filtered (a4) to facilitate threshold-based detection of tau pSer262-positive objects (red outline in a5). These outlines were then loaded onto the raw images to quantify original tau pSer262 signal (red outline in a6). AF: autofluorescence. Scale bar: 20 μm. Online Source 11 Example of detecting ThioS-positive amyloid-β but not NFTs. Image a displays the co-labeling of ThioS (green) and HT7 (red), while images b and c, respectively, show single channel images. ThioS shows intense labeling of plaque-associated β-sheets (b, asterisk) whereas tangles are only weakly labeled (c, arrows) (c). A combination of threshold-based identification of ThioS and size restriction (d‘, green rectangle) enables quantification of ThioS+ plaque labeling (red highlighted) but not tangles (d). ThioS: ThioflavinS. Scale bar: 20 μm. (PDF 599 kb

Dreidimensionale Observierung atmosphärischer Prozesse in Städten – 3DOSchlussbericht des Verbundvorhabens 3DOThree-dimensional observation and modeling of atmospheric processes in cities – 3DOfinal report for joint project 3DO

Ziel des BMBF-Programms 'Stadtklima im Wandel' war die Entwicklung, Validierung und Anwendung eines gebäudeauflösenden Stadtklimamodells für ganze Städte. Das Verbundprojekt 3DO übernahm die dem Modul B zugeordneten Forschungsaufgaben: Aufbereitung vorhandener Daten aus der Langzeitbeobachtung (LTO), Aufbau neuer Messstationen, Gewinnung neuer dreidimensionaler atmosphärischer Daten und die Entwicklung neuer Konzepte z.B. zur Modellevaluation. Untersucht wurden der Aufbau der atmosphärischen Grenzschicht, die Charakteristik der meteorologischen Parameter und deren Einfluss auf das thermische Empfinden des Menschen. Ein einheitlicher [UC]2-Datenstandard sowie Analysewerkzeuge wurden entwickelt und in ein Datenmanagementsystem und eine Wissensplattform für den modulübergreifenden Austausch integriert.Aim of the BMBF-Programme 'Urban Climate under Change' was development, validation and application of a building-resolving urban climate model for entire cities. The joint project 3DO took over the research tasks assigned to module B: Preparation of existing data from long-term observation (LTO), deployment of new measuring stations, acquisition of new three-dimensional atmospheric data and new concepts, e.g. for model evaluation. The structure of the atmospheric boundary layer, characteristics of meteorological parameters and their influence on the thermal sensation of humans were investigated. A uniform [UC]2 data standard as well as analysis tools were developed and integrated into a data management system and a knowledge base for cross-module exchange

Dreidimensionale Observierung atmosphärischer Prozesse in Städten – 3DOSchlussbericht des Verbundvorhabens 3DOThree-dimensional observation and modeling of atmospheric processes in cities – 3DOfinal report for joint project 3DO

Ziel des BMBF-Programms 'Stadtklima im Wandel' war die Entwicklung, Validierung und Anwendung eines gebäudeauflösenden Stadtklimamodells für ganze Städte. Das Verbundprojekt 3DO übernahm die dem Modul B zugeordneten Forschungsaufgaben: Aufbereitung vorhandener Daten aus der Langzeitbeobachtung (LTO), Aufbau neuer Messstationen, Gewinnung neuer dreidimensionaler atmosphärischer Daten und die Entwicklung neuer Konzepte z.B. zur Modellevaluation. Untersucht wurden der Aufbau der atmosphärischen Grenzschicht, die Charakteristik der meteorologischen Parameter und deren Einfluss auf das thermische Empfinden des Menschen. Ein einheitlicher [UC]2-Datenstandard sowie Analysewerkzeuge wurden entwickelt und in ein Datenmanagementsystem und eine Wissensplattform für den modulübergreifenden Austausch integriert.Aim of the BMBF-Programme 'Urban Climate under Change' was development, validation and application of a building-resolving urban climate model for entire cities. The joint project 3DO took over the research tasks assigned to module B: Preparation of existing data from long-term observation (LTO), deployment of new measuring stations, acquisition of new three-dimensional atmospheric data and new concepts, e.g. for model evaluation. The structure of the atmospheric boundary layer, characteristics of meteorological parameters and their influence on the thermal sensation of humans were investigated. A uniform [UC]2 data standard as well as analysis tools were developed and integrated into a data management system and a knowledge base for cross-module exchange