Biology subjects

Rabe, K. S.

Publications and source records attributed to Rabe, K. S..

6 recordsLinked to original sources

bioRxiv2026

Temporal emergence of functional dark matter in microbial responses to PFAS revealed by materials-based cultivation

Microbial responses to xenobiotic compounds are difficult to resolve due to environmental complexity and limited functional annotation. Here, we establish a materials-based cultivation framework using macroporous elastomeric silicone foams (MESIF) to capture microbial adaptation across environmental contexts and timescales. Using glyphosate as a model compound and per- and polyfluoroalkyl substances (PFAS) as a poorly understood class, we show that responses differ depending on the availability of established metabolic pathways. Glyphosate exposure induced rapid, pathway-specific functional enrichment with minimal taxonomic change. In contrast, PFAS exposure did not yield consistent taxonomic or annotation-based signals but instead produced responses that emerged over time and were primarily detectable at protein and genome-resolved levels. LC-MS analyses revealed transformation dynamics, including formation of shorter-chain products. These responses were not explained by known degrader taxa but involved uncharacterized proteins and microbial populations, highlighting the extent of functional "dark matter" in microbial responses to persistent contaminants.

microbiology↗

bioRxiv2022

A genetically-encoded three-colour stress biosensor reveals multimodal response at single cell level and spatiotemporal dynamics of biofilms

The plethora of chemical, physical, and biological factors that can damage microbial cells has triggered the evolution of sophisticated stress response (SR) mechanisms. While individual SR pathways have been monitored with genetically encoded reporters, sensor concepts for the detection of multimodal effects of stressing conditions in living microorganisms are still lacking. Orthogonally detectable red, green, and blue fluorescent proteins combined in a single vector system, dubbed RGB-S reporter, enable the simultaneous, independent and real-time analysis of the stress response in Escherichia coli to physiological stress, genotoxicity, and cytotoxicity. The sensor system can be read out via conventional fluorescence microscopy or microtiter plate analysis and can also be combined with Fluorescent Activated Cell Sorting (FACS) and subsequent transcriptome analysis. Various stressors, such as the biotechnologically relevant 2-propanol, lead to the activation of one, two or all three SRs, which can have a significant impact on non-stress-related metabolic pathways. Implemented in microfluidic cultivation with confocal fluorescence microscopy imaging, the technology enabled spatiotemporal analysis of live biofilms to discover stratified subpopulations of bacteria with heterogeneous stress responses.

microbiology↗

bioRxiv2019

Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

The optimal growth temperature (OGT) of organisms is an important index to estimate the stability of enzymes encoded in their genomes. However, experimental determination of OGT for microorganisms that cannot be cultivated is difficult. Here, we report on the development of a machine learning model that can accurately predict OGT directly from proteome-wide 2-mer amino acid composition. We make use of this model to predict OGTs for 1,438 microorganisms. In a subsequent step we combine OGT data with amino acid composition of individual enzymes to develop a second machine learning model for prediction of enzyme temperature optima (Topt). The resulting model is far superior to using OGT alone for estimating Topt in a dataset of 2,609 enzymes. Finally, we predict Topt for 6.5 million enzymes, covering 4,447 EC numbers, and make the resulting dataset available for researchers, enabling simple identification of enzymes that are potentially functional at extreme temperatures.

bioinformatics↗

bioRxiv2017

Self-assembling all-enzyme hydrogels for biocatalytic flow processes

We describe the construction of binary self-assembling all-enzyme hydrogels that are comprised entirely of two tetrameric globular enzymes, the stereoselective dehydrogenase LbADH and the cofactor-regenerating glucose 1-dehydrogenase GDH. The enzymes were genetically fused with a SpyTag or SpyCatcher domain, respectively, to generate two complementary homo-tetrameric building blocks that polymerise under physiological conditions into porous hydrogels. The biocatalytic gels were used for the highly stereoselective reduction of a prochiral diketone substrate where they showed the typical behaviour of the coupled kinetics of coenzyme regenerating reactions in the substrate channelling regime. They effectively sequestrate the NADPH cofactor even under continuous flow conditions. Owing to their sticky nature, the gels can be readily mounted in simple microfluidic reactors without the need for supportive membranes. The reactors revealed extraordinary high space-time yields with nearly quantitative conversion (>95%), excellent stereoselectivity (d.r. > 99:1), and total turnover numbers of the expensive cofactor NADP(H) that are amongst the highest values ever reported.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC=\"FIGDIR/small/240325_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@19a66b9org.highwire.dtl.DTLVardef@1ce1a41org.highwire.dtl.DTLVardef@1dac96org.highwire.dtl.DTLVardef@2db317_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2017

Cytosolic delivery of large supramolecular proteincomplexes arranged on DNA nanopegboards

A generic methodology for cytosolic delivery of large supramolecular multiprotein complexes into living cells is described that takes advantage of the highly-controllable bottom-up fabrication of protein-decorated DNA nanostructures and the microfluidic \"cell squeezing\" technique. Therein, cells are deformed upon passage through a narrow constriction leading to formation of transient holes in the cell membrane that enable the diffusion of the protein-DNA nanostructures from the surrounding buffer into the cytosol. A diverse set of multiprotein complexes was assembled on DNA origami nanostructures using streptavidin and the sensitive glucose sensor protein FLIP as model systems. We demonstrate that our approach allows for the direct cytosolic delivery of these multifunctional protein complexes into the cytosol of HeLa cells. We also demonstrate that targeting groups can be incorporated into the protein-DNA nanoassemblies to enable their intracellular targeting to cytosolic compartments, such as the cytoskeleton or nucleus. We believe that this methodology will open up novel strategies for research in fundamental cell biology, such as the reverseengineering of the supramolecular machinery involved in gene regulation, cell signalling, or cell division. Furthermore, direct applications in immunotherapy can be foreseen.

cell biology↗

bioRxiv2017

Machine-assisted cultivation and analysis of biofilms

Biofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases as feeding sources and offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platforms performance by monitoring the self-organized separation of mixed cultures along autonomously created gradients, the productivity of biofilms along the microfluidic channel and the enrichment of microbial nanoorganisms.

microbiology↗