Biology subjects

Fiedler, K.

Publications and source records attributed to Fiedler, K..

4 recordsLinked to original sources

bioRxiv2024

A snapshot of the Physcomitrella N-terminome reveals N-terminal methylation of organellar proteins

Post- or co-translational N-terminal modifications of proteins influence their half-life as well as mediating protein sorting to organelles via cleavable N-terminal sequences that are recognized by the respective translocation machinery. Here, we provide an overview on the current modification state of the N-termini of over 4500 proteins from the model moss Physcomitrella (Physcomitrium patens) using a compilation of 24 N-terminomics datasets. Our data reveal distinct proteoforms and modification states and confirm predicted targeting peptide cleavage sites of 1144 proteins localized to plastids and the thylakoid lumen, to mitochondria, and to the secretory pathway. Additionally, we uncover extended N-terminal methylation of mitochondrial proteins. Moreover, we identified PpNTM1 (P. patens alpha N-terminal protein methyltransferase 1) as a candidate for protein methylation in plastids, mitochondria and the cytosol. These data can now be used to optimize computational targeting predictors, for customized protein fusions and their targeted localization in biotechnology, and offer novel insights into potential dual targeting of proteins. Key messageAnalysis of the N-terminome of Physcomitrella reveals N-terminal monomethylation of nuclear encoded, mitochondria-localized proteins. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/598444v3_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1f31702org.highwire.dtl.DTLVardef@6b9ce6org.highwire.dtl.DTLVardef@109c041org.highwire.dtl.DTLVardef@12cf83e_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2024

A Synergistic Desmin-SPARC Axis Regulates Cardiac Stem Cell Differentiation and Promotes Cardiomyogenesis through Autocrine Regulation

BACKGROUNDThe mammalian heart contains cardiac stem cells throughout life, but it has not been possible to harness or stimulate these cells to repair damaged myocardium in vivo. Assuming physiological relevance of these cells, which have evolved and have been maintained throughout evolution, we are investigating their function using mouse cardiac stem cell lines as an in vitro model system. METHODSHere we use genetically modified embryonic stem cells and cardiac stem cells from the mouse as model systems to study the influence of desmin and Secreted Protein Acidic and Rich in Cysteine (SPARC) on cardiomyogenesis in embryoid bodies and cardiac bodies. We analyze their expression in self-renewing and differentiating stem cells by fluorescence microscopy, RT-qPCR, quantitative Western blotting and fluorescence activated cell sorting, and assess their influence on the expression of myocardial transcription factors. RESULTSIn embryoid bodies, desmin induces expression and secretion of SPARC, which promotes cardiomyogenesis. Cardiac stem cells secrete substantial amounts of SPARC, which also promotes cardiomyogenesis in a concentration-dependent, autocrine manner and promotes expression of myocardial transcription factors and desmin. Desmin and SPARC interact genetically and form a positive feedback loop and secreted SPARC negatively influences sparc mRNA expression. Finally, SPARC rescues cardiomyogenic desmin-haploinsufficiency in cardiac stem cells in a glycosylation-dependent manner, increases the phosphorylation of Smad2 and induces the expression of gata4, nkx2.5 and mef2C. CONCLUSIONSDemonstration that desmin-induced autocrine secretion of SPARC in cardiac stem cells promotes cardiomyogenesis raises the possibility that a physiological function of cardiac stem cells in the adult and aging heart may be the gland-like secretion of factors such as SPARC that modulate age-related and adverse environmental influences and thereby contribute to cardiac homeostasis throughout life.

developmental biology↗

bioRxiv2017

Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn’s Disease

Inflammatory bowel disease (IBD), clinically defined as Crohns disease (CD), ulcerative colitis (UC), or IBD-unclassified, results in chronic inflammation of the gastrointestinal tract in genetically susceptible hosts. Pediatric onset IBD represents [≥]25% of all IBD diagnoses and often presents with intestinal stricturing, perianal disease, and failed response to conventional treatments. NOD2 was the first and is the most replicated locus associated with adult IBD, to date. To determine the role of NOD2 and other genes in pediatric IBD, we performed whole-exome sequencing on a cohort of 1,183 patients with pediatric onset IBD (ages 0-18.5 years). We identified 92 probands who were homozygous or compound heterozygous for rare and low frequency NOD2 variants accounting for approximately 8% of our cohort, suggesting a Mendelian recessive inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance of NOD2 alleles in adult IBD patients from the Regeneron Genetics Center (RGC)-Geisinger Health System DiscovEHR study, which links whole exome sequences to longitudinal electronic health records (EHRs) from 51,289 participants. We found that ~7% of cases in this adult IBD cohort, including ~10% of CD cases, can be attributed to recessive inheritance of NOD2 variants, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that 14% of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. Collectively, our findings show that recessive inheritance of rare and low frequency deleterious NOD2 variants account for 7-10% of CD cases and implicate NOD2 as a Mendelian disease gene for early onset Crohns Disease.\n\nAuthor SummaryPediatric onset inflammatory bowel disease (IBD) represents [≥]25% of IBD diagnoses; yet the genetic architecture of early onset IBD remains largely uncharacterized. To investigate this, we performed whole-exome sequencing and rare variant analysis on a cohort of 1,183 pediatric onset IBD patients. We found that 8% of patients in our cohort were homozygous or compound heterozygous for rare or low frequency deleterious variants in the nucleotide binding and oligomerization domain containing 2 (NOD2) gene. Further investigation of whole-exome sequencing of a large clinical cohort of adult IBD patients uncovered recessive inheritance of rare and low frequency NOD2 variants in 7% of cases and that the relative risk for NOD2 variant homozygosity has likely been underestimated. While it has been reported that having >1 NOD2 risk alleles is associated with increased susceptibility to Crohns Disease (CD), our data formally demonstrate what has long been suspected: recessive inheritance of NOD2 alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Our data suggest that a subset of IBD-CD patients with early disease onset is characterized by recessive inheritance of NOD2 alleles, which has important implications for the screening, diagnosis, and treatment of IBD.

genetics↗

bioRxiv2016

VIP36 preferentially binds to core-fucosylated N-glycans: a molecular docking study

Alpha 1-6 fucosyltransferase (Fut8) is known for its properties as an enhancer of nonsmall cell lung cancer metastasis and as a suppressor in hepatocellular carcinoma cells (Hep3B). Promising candidates of affected molecules include E-cadherin. In its absence, during epithelial-mesenchymal transition, the pathway triggers signaling to the nucleus via {beta}-catenin-TCF/LEF. Contrarily, in less metastatic tumors, Fut8 stimulates cell-cell adhesion. Regulated classes of molecules could also include the sorting machinery of polarized epithelial cells, sorted ligands or both, that may be altered in cellular transformation. I have analyzed here the cargo receptor VIP36 (Vesicular-integral membrane protein of 36 kD) for carbohydrate interaction. It has been described as a lectin in the ERGIC (endoplasmic reticulum-Golgi intermediate compartment), Golgi apparatus and plasma membrane. The docking reveals top-interacting carbohydrates of the N-glycan and O-glycan class that encompass N-linked glycans of high mannose and equally complex type which likely function as sorted ligands in epithelial cells. O-glycans score lower and include core 2 residue binding. I show that fucose core modifications by Fut8 stimulate binding of N-linked glycans to VIP36, which is known to be different from binding of galectins 3 and 9. This suggests that Fut8-upregulation may directly alter the affinity of sorted cargo and may enhance the sorting to the apical pathway as exemplified in hepatocytes and traffic to bile. High affinity binding of the ganglioside GM1 carbohydrate headgroup to VIP36 suggests a linkage with protein and glycosphingolipid apical transfer in epithelial cells. Thus, this fundamental approach with large scale docking of 165 carbohydrates including 19 N-glycan high mannose, 17 Nglycan hybrid, 9 N-glycan complex, 17 O-glycan core, 27 Sialoside, 25 Fucoside and 51 other glycan residues suggests, that linked cargo-receptor apical transport may provide a path to epithelial polarization that may be modulated by core fucosylation.

biochemistry↗