Biology subjects

Sommer, F.

Publications and source records attributed to Sommer, F..

25 records · Page 2Linked to original sources

bioRxiv2020

Functional and molecular early enteric biomarkers for Parkinson's disease in mice and men

Parkinsons disease (PD) usually has a late clinical onset. The lack of early biomarkers for the disease represents a major challenge for developing timely treatment interventions. Here, we use an -synuclein-overexpressing transgenic (Th-1-SNCA-A30P) mouse model of PD to identify appropriate candidate markers in the gut for early stages of PD before hallmark symptoms begin to manifest. A30P mice did not show alterations in gait parameters at 2 months of age, and these mice were therefore defined as pre-symptomatic A30P mice (psA30P). We discovered early functional motility changes in the gut and early molecular dysregulations in the myenteric plexus of psA30P mice by comparative protein and miRNA profiling and cell culture experiments. We found that the proteins neurofilament light chain, vesicle-associated membrane protein 2 and calbindin 2, together with the miRNAs that regulate them, are potential biomarkers of early PD that may facilitate timely treatment and/or prevention of PD in men.

neuroscience↗

bioRxiv2020

Overexpression of sedoheptulose-1,7-bisphosphatase enhances photosynthesis in Chlamydomonas reinhardtii and has no effect on the abundance of other Calvin-Benson cycle enzymes

The productivity of plants and microalgae needs to be increased to feed the growing world population and to promote the development of a low-carbon economy. This goal can be achieved by improving photosynthesis via genetic engineering. In this study, we have employed the Modular Cloning strategy to overexpress the Calvin-Benson cycle (CBC) enzyme sedoheptulose-1,7 bisphosphatase (SBP1) up to 3-fold in the unicellular green alga Chlamydomonas reinhardtii. The protein derived from the nuclear transgene represented [~]0.3% of total cell protein. Photosynthetic rate and growth were significantly increased in SBP1-overexpressing lines under high-light and high-CO2 conditions. Absolute quantification of the abundance of all other CBC enzymes by the QconCAT approach revealed no consistent differences between SBP1-overexpressing lines and the recipient strain. This analysis also revealed that the eleven CBC enzymes represent 11.9% of total cell protein in Chlamydomonas. Here the range of concentrations of CBC enzymes turned out to be much larger than estimated earlier, with a 128-fold difference between the most abundant CBC protein (rbcL) and the least abundant (triose phosphate isomerase). Accordingly, the concentrations of the CBC intermediates are often but not always higher than the binding site concentrations of the enzymes for which they act as substrates. The enzymes with highest substrate to binding site ratios might represent good candidates for overexpression in subsequent engineering steps.

plant biology↗

bioRxiv2020

Vernalization alters sugar beet (Beta vulgaris) sink and source identities and reverses phloem translocation from taproots to shoots

During vegetative growth, biennial sugar beets maintain a steep gradient between the shoot (source) and the sucrose-storing taproot (sink). To shift from vegetative to generative growth, they require a chilling phase, called vernalization. Here, we studied sugar beet sink-source dynamics upon cold temperature-induced vernalization and revealed a pre-flowering taproot sink to source reversal. This transition is induced by transcriptomic and functional reprogramming of sugar beet tissue, resulting in a reversal of flux direction in long distance transport system, the phloem. As a key process for this transition, vacuolar sucrose importers and exporters, BvTST2;1 and BvSUT4, are oppositely regulated, leading to re-mobilization of sugars from taproot storage vacuoles. Concomitant changes in the expression of floral regulator genes suggest that the now deciphered processes are a prerequisite for bolting. Our data may thus serve dissecting metabolic and developmental triggers for bolting, which are potential targets for genome editing or breeding approaches.

plant biology↗

bioRxiv2019

Antagonism between regular and atypical Cxcr3 receptors regulates macrophage migration during infection and injury in zebrafish

The CXCR3-CXCL11 chemokine-signaling axis plays an essential role in infection and inflammation by orchestrating leukocyte trafficking in human and animal models, including zebrafish. Atypical chemokine receptors (ACKRs) play a fundamental regulatory function in signaling networks by shaping chemokine gradients through their ligand scavenging function, while being unable to signal in the classic G-protein-dependent manner. Two copies of the CXCR3 gene in zebrafish, cxcr3.2 and cxcr3.3, are expressed on macrophages and share a highly conserved ligand-binding site. However, Cxcr3.3 has structural characteristics of ACKRs indicative of a ligand-scavenging role. In contrast, we previously showed that Cxcr3.2 is an active CXCR3 receptor since it is required for macrophage motility and recruitment to sites of mycobacterial infection. In this study, we generated a cxcr3.3 CRISPR-mutant to functionally dissect the antagonistic interplay between the cxcr3 paralogs in the immune response. We observed that cxcr3.3 mutants are more susceptible to mycobacterial infection, while cxcr3.2 mutants are more resistant. Furthermore, macrophages in the cxcr3.3 mutant are more motile, show higher activation status, and are recruited more efficiently to sites of infection or injury. Our results suggest that Cxcr3.3 is an ACKR that regulates the activity of Cxcr3.2 by scavenging common ligands and that silencing the scavenging function of Cxcr3.3 results in an exacerbated Cxcr3.2 signaling. In human, splice variants of CXCR3 have antagonistic functions and CXCR3 ligands also interact with ACKRs. Therefore, in zebrafish, an analogous regulatory mechanism appears to have evolved after the cxcr3 gene duplication event, through diversification of conventional and atypical receptor variants.\n\nSummary sentenceCXCR3 paralogue with structural characteristics of atypical chemokine receptors regulates the activity of a conventional receptor involved in macrophage motility by scavenging shared ligands.

immunology↗

bioRxiv2019

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

BackgroundThe interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These interdependencies inspired a new view of multicellular organisms as \"metaorganisms\". The goal of the Collaborative Research Center \"Origin and Function of Metaorganisms\" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.\n\nMethodsIn order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon- and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.\n\nConclusionWhile 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods and that metagenomic shotgun results are largely dependent on the employed pipeline. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

microbiology↗

bioRxiv2019

High fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine

Over-consumption of high-fat diets (HFDs) is associated with several pathologies. Although the intestine is the organ that comes into direct contact with all diet components, the impact of HFD has mostly been studied in organs that are linked to obesity and obesity related disorders. We used Drosophila as a simple model to disentangle the effects of a HFD on the intestinal structure and physiology from the plethora of other effects caused by this nutritional intervention. Here, we show that a HFD triggers activation of intestinal stem cells in the Drosophila midgut. This stem cell activation was transient and preceded by induction of JNK signaling in enterocytes. JNK (basket) within enterocytes was essential for activation of stem cells in response to a HFD. Moreover, this nutritional intervention leads to upregulation of the cytokine upd3 in enterocytes, a reaction that is known to trigger STAT signaling in intestinal stem cells followed by their activation. We also showed that the indigenous microbiota was essential for HFD-induced stem cell activation because this response was blunted in germ-free flies lacking a microbiota. Moreover, chronic HFD feeding of flies markedly altered both the microbiota composition and bacterial load. Although HFD-induced stem cell activity was transient, long-lasting changes to the cellular composition, including a substantial increase in the number of enteroendocrine cells, were observed. Taken together, a HFD enhances stem cell activity in the Drosophila gut and this effect is completely reliant on the indigenous microbiota and also dependent on JNK signaling within intestinal enterocytes.\n\nAuthor summaryHigh-fat diets have been associated with a plethora of morbidities. The major research focus has been on its effects on obesity related disorders, mostly omitting the intestine, although it is the organ that makes the first contact with all diet components. Here, we aimed to understand the direct effects of HFD on the intestine itself. Using Drosophila as a model, we showed that HFD induced a transient activation of intestinal stem cells. This response completely depended on JNK signaling in enterocytes. Mechanistically, we found that HFD induces JNK signaling in enterocytes, which triggers production of the cytokine upd3. This, in turn activates STAT signaling in intestinal stem cells, leading to their activation. Surprisingly, we found that a HFD triggered induced stem cell activation critically depends on the indigenous microbiota, as in germ free flies this reaction was completely abolished. Moreover, HFD changed both, composition and abundance of the microbiota. As fecal transfer experiments failed to recapitulate the HFD phenotype, we assume that the increased bacterial load is the major cause for the HFD triggered stem cell activation in the intestine.

physiology↗

bioRxiv2018

Hetero-oligomeric CPN60 resembles highly symmetric group I chaperonin structure revealed by Cryo-EM

The chloroplast chaperonin system is indispensable for the biogenesis of Rubisco, the key enzyme in photosynthesis. Using Chlamydomonas reinhardtii as the model system, we revealed that chloroplast chaperonin is consisted of CPN60, CPN60{beta}1, and CPN60{beta}2, and co-chaperonin is composed of three subunits CPN20, CPN11 and CPN23 in vivo. CPN20 homo-oligomers and all possible other chloroplast co-chaperonin hetero-oligomers are functional, but only CPN11/20/23-CPN60{beta}1{beta}2 pair can fully replace GroES/GroEL in E. coli at stringent growth condition. Endogenous CPN60 was purified and its stoichiometry was determined to be 6:2:6 for CPN60:CPN60{beta}1:CPN60{beta}2. The cryo-EM structures of endogenous CPN60{beta}1{beta}2/ADP and CPN60{beta}1{beta}2/co-chaperonin/ADP were solved at resolutions of 4.06 [A] and 3.82[A], respectively. In both hetero-oligomeric complexes the chaperonin subunits within each ring are highly symmetric. The chloroplast co-chaperonin CPN11/20/23 formed seven GroES-like domains through hetero-oligomerization which symmetrically interact with CPN60{beta}1{beta}2. Our structures also reveal an uneven distribution of roof-like structures in the dome-shaped CPN11/20/23 and potentially diversified surface properties in the folding cavity of CPN60{beta}1{beta}2 that might enable the chloroplast chaperonin system to assist in the folding of specific substrates.

biochemistry↗