Biology subjects

Schulze, S.

Publications and source records attributed to Schulze, S..

24 records · Page 2Linked to original sources

bioRxiv2020

Haloferax volcanii immersed liquid biofilms develop independently of known biofilm machineries and exhibit rapid honeycomb pattern formation

The ability to form biofilms is shared by many microorganisms, including archaea. Cells in a biofilm are encased in extracellular polymeric substances that typically include polysaccharides, proteins, and extracellular DNA, conferring protection while providing a structure that allows for optimal nutrient flow. In many bacteria, flagella and evolutionarily conserved type IV pili are required for the formation of biofilms on solid surfaces or floating at the air-liquid interface of liquid media. Similarly, in many archaea it has been demonstrated that type IV pili and, in a subset of these species, archaella are required for biofilm formation on solid surfaces. Additionally, in the model archaeon Haloferax volcanii, chemotaxis and AglB-dependent glycosylation play important roles in this process. H. volcanii also forms immersed biofilms in liquid cultures poured into Petri dishes. This study reveals that mutants of this haloarchaeon that interfere with the biosynthesis of type IV pili or archaella, as well as a chemotaxis-targeting transposon and aglB-deletion mutants, lack obvious defects in biofilms formed in liquid cultures. Strikingly, we have observed that these liquid-based biofilms are capable of rearrangement into honeycomb-like patterns that rapidly form upon removal of the Petri dish lid, a phenomenon that is not dependent on changes in light or oxygen concentration but can be induced by controlled reduction of humidity. Taken together, this study demonstrates that H. volcanii requires novel, as-yet-unidentified strategies for immersed liquid biofilm formation and also exhibits rapid structural rearrangements. ImportanceThis first molecular biological study of archaeal immersed liquid biofilms advances our basic-biological understanding of the model archaeon Haloferax volcanii. Data gleaned from this study also provide an invaluable foundation for future studies to uncover components required for immersed liquid biofilms in this haloarchaeon and also potentially for liquid biofilm formation in general, which is poorly understood compared to the formation of biofilms on surfaces. Moreover, this first description of rapid honeycomb pattern formation is likely to yield novel insights into the underlying structural architecture of extracellular polymeric substances and cells within immersed liquid biofilms.

microbiology↗

bioRxiv2019

LIPID ANCHORING OF ARCHAEOSORTASE SUBSTRATES AND MID-CELL GROWTH IN HALOARCHAEA

The archaeal cytoplasmic membrane provides an anchor for many surface proteins. Recently, a novel membrane anchoring mechanism involving a peptidase, archaeosortase A (ArtA) and C-terminal lipid attachment of surface proteins was identified in the model archaeon Haloferax volcanii. ArtA is required for optimal cell growth and morphogenesis, and the S-layer glycoprotein (SLG), the sole component of the H. volcanii cell wall, is one of the targets for this anchoring mechanism. However, how exactly ArtA function and regulation control cell growth and mor-phogenesis is still elusive. Here, we report that archaeal homologs to the bacterial phos-phatidylserine synthase (PssA) and phosphatidylserine decarboxylase (PssD) are involved in ArtA-dependent protein maturation. H. volcanii strains lacking either HvPssA or HvPssD exhibited motility, growth and morphological phenotypes similar to those of {triangleup}artA. Moreover, we showed the loss of covalent lipid attachment to SLG in the {triangleup}hvpssA mutant and that proteolytic cleavage of the ArtA substrate HVO_0405 was blocked in the {triangleup}hvpssA and {triangleup}hvpssD strains. Strikingly, ArtA, HvPssA, and HvPssD GFP-fusions co-localized to the mid position of H. volcanii cells, strongly supporting that they are involved in the same pathway. Finally, we have shown that the SLG is also recruited to the mid cell prior to being secreted and lipid-anchored at the cell outer surface. Collectively, our data suggest haloarchaea use the mid cell as the main surface processing hotspot for cell elongation, division and shape determination.

cell biology↗

bioRxiv2019

Novel insights into N-glycan fucosylation and core xylosylation in C. reinhardtii

Chlamydomonas reinhardtii N-glycans carry plant typical {beta}1,2-core xylose, 1,3-fucose residues as well as plant atypical terminal {beta}1,4-xylose and methylated mannoses. In a recent study, XylT1A was shown to act as core xylosyltransferase, whereby its action was of importance for an inhibition of excessive Man1A dependent trimming. N-Glycans found in a XylT1A/Man1A double mutant carried core xylose residues, suggesting the existence of a second core xylosyltransferase in C. reinhardtii. To further elucidate enzymes important for N-glycosylation, novel single knockdown mutants of candidate genes involved in the N-glycosylation pathway were characterized. In addition, double, triple and quadruple mutants affecting already known N-glycosylation pathway genes were generated. By characterizing N-glycan compositions of intact N-glycopeptides from these mutant strains by mass spectrometry, a candidate gene encoding for a second putative core xylosyltransferase (XylT1B) was identified. Additionally, the role of a putative fucosyltransferase was revealed. Mutant strains with knockdown of both xylosyltransferases and the fucosyltransferase resulted in the formation of N-glycans with strongly diminished core modifications. Thus, the mutant strains generated will pave the way for further investigations on how single N-glycan core epitopes modulate protein function in C. reinhardtii.\n\nSignificance StatementOur data provide novel insights into the function of XylT1B and FucT in C. reinhardtii as N-glycan core modifying enzymes. In the course of our study, different mutants were created by genetic crosses showing either varying or a lack of N-glycan core modification, enabling comparative analyses in relation to single N-glycan core epitope and overall protein function in C. reinhardtii.

plant biology↗

bioRxiv2019

Differences in player position running velocity at lactate thresholds among male professional German soccer players

This study investigated the differences in running velocities at specific lactate thresholds among male German soccer players. One hundred fifty-two professional (3rd league: n=82; 4th league: n=70) male soccer players (mean {+/-} SD; age: 24.7 {+/-} 4.38 years, body mass: 80.7 {+/-} 7.36 kg, body height: 1.83 {+/-} 0.06 m) volunteered for the investigation. Players were categorized as goalkeepers, central defenders, central midfielders, wings and forwards. Players completed a treadmill test, at incremental speeds, to determine running velocity at different blood lactate concentrations (v2=2 mmol/l; v4=4 mmol/l; v6=6 mmol/l). Results indicate that, wings displayed the lowest body mass (76.2 {+/-} 6.08 kg) and body height (1.79 {+/-} 0.06 m). In contrast, goalkeepers were the tallest athletes in the whole sample (1.90 {+/-} 0.03 m), forwards were the heaviest players (85.4 {+/-} 6.03 kg). In addition, we detected the largest difference between positions for running velocity at the lactate threshold v2 (p=0.002). The running data revealed that only the goalkeepers had significantly lower velocities at the lactate thresholds compared to the field players. The central midfielders showed the highest performance level at the lactate thresholds (v2: 12.5 {+/-} 1.20 km/h; v4: 15.2 {+/-} 1.14 km/h; v6: 16.6 {+/-} 1.13 km/h). In conclusion, this study provides soccer and position-specific reference data for the performance of male professional German soccer players in order to evaluate the running performance in a valid way. In this context, it is necessary to extend the database for the second and first league. Furthermore, it is important to assess the running performance during competition matches over the entire season in order to validate the endurance test performance data.

physiology↗

bioRxiv2018

Cell type-dependent differential activation of ERK by oncogenic KRAS or BRAF in the mouse intestinal epithelium

Mutations activating the KRAS GTPase or the BRAF kinase are frequent in colorectal cancer and are thought to constitutively activate the terminal mitogen-activated protein kinase, ERK. Using mass cytometry, we found graded phosphorylation of ERK anti-correlated with cell differentiation in patient-derived colorectal cancer organoids, independent of KRAS mutational status. Reporter, single cell transcriptome and mass cytometry analyses showed that transgenic KRASG12V activated ERK in a cell type-specific pattern in mouse intestinal organoids. In contrast, transgenic BRAFV600E triggered high ERK activity and downstream gene expression in all intestinal cell types, followed by epithelial disorganisation. Quantitative network modelling from perturbation data revealed that activation of ERK is shaped by cell type-specific MEK to ERK feed forward and negative feedback signalling. We identified dual-specificity phosphatases as candidate modulators of ERK activity between intestinal cell types. Furthermore, we found that oncogenic KRAS, together with {beta}-Catenin, favoured expansion of crypt cells with high ERK activity. Our experiments highlight key differences between ERK activity elicited by the BRAF or KRAS oncogenes in colorectal cancer and find unexpected heterogeneity in a signalling pathway with fundamental relevance for cancer therapy.

cell biology↗

bioRxiv2017

LASSIM - a network inference toolbox for genome-wide mechanistic modeling

Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is the first general mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady states and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. LASSIM models are built in two steps, where each step can integrate multiple data-types, and the method is implemented as a general-purpose toolbox using the PyGMo Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM first infers a non-linear ODE system of the pre-specified core genes. Second, LASSIM optimizes the parameters that models the regulation of peripheral genes by core-system genes in parallel. We showed the usefulness of this method by applying LASSIM to infer a large-scale nonlinear model of naive Th2 differentiation, made possible by integrating Th2 specific bindings, time-series and six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models with truly systems-level data. We exemplified the advantage by inferring the first mechanistically motivated genome-wide model of the Th2 transcription regulatory system, which plays an important role in the progression of immune related diseases.\n\nAuthor summaryThere are excellent methods to mathematically model time-resolved biological data on a small scale using accurate mechanistic models. Despite the rapidly increasing availability of such data, mechanistic models have not been applied on a genome-wide level due to excessive runtimes and the non-identifiability of model parameters. However, genome-wide, mechanistic models could potentially answer key clinical questions, such as finding the best drug combinations to induce an expression change from a disease to a healthy state.\n\nWe present LASSIM, which is a toolbox built to infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the inference into small solvable subproblems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces the time required for the computation to finish.

systems biology↗