Biology subjects

Muehlhaus, T.

Publications and source records attributed to Muehlhaus, T..

10 recordsLinked to original sources

bioRxiv2026

Elab2ARC: A Browser-Based Workspace for Converting Free-Text Protocols into rich FAIR digital objects

Electronic laboratory notebooks (ELNs) are widely used in the life sciences, but their notebook format limits machine-readability and FAIR compliance. Consequently, researchers often spend significant manual effort restructuring ELN records into publication-ready outputs. We present elab2ARC, a browser-based workspace that automates the conversion of open-source eLabFTW records into Annotated Research Contexts (ARCs)-- version-controlled, ISA-compliant research objects. Using the eLabFTW API, elab2ARC retrieves administrative metadata, protocols, and attachments, reorganising them into ISA-compliant tables and linked datasets. All processing occurs client-side, ensuring user data control before submission to the PLANTdataHUB repository. An optional LLM-assisted workflow extracts structured metadata from free-text protocols, providing editable drafts while preserving human oversight. Designed for use at project completion, elab2ARC reuses existing ELN documentation without disrupting daily laboratory practice. It offers a practical route to FAIR-aligned sharing, publication, and long-term archiving of life-science experimental records. Availability and implementationelab2ARC is freely accessible at https://nfdi4plants.org/elab2arc/. The source code is available at https://github.com/nfdi4plants/elab2arc under a GPL-3.0 license. Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2025

Heterooligomerization drives structural plasticity of eukaryotic peroxiredoxins

Peroxiredoxins are highly conserved thiol peroxidases essential for peroxide detoxification, redox signaling, and chaperone activity. Prx1/AhpC-type peroxiredoxins are found throughout the eukaryotic kingdom, where multiple isoforms frequently coexist within the same cell and even in the same subcellular compartment. Long thought to form exclusively homooligomeric structures, we reveal that heterooligomerization is a conserved and important feature of eukaryotic Prx1/AhpC-type peroxiredoxins. We demonstrate that heterooligomer formation modulates peroxoredoxin oligomeric state and enhances structural stability. In yeast, Tsa1-Tsa2 peroxiredoxin heterodecamers form in response to oxidative stress and incorporated Tsa2 stabilizes the decameric state. Beyond yeast, we show that human PRDX1 and PRDX2, as well as plant and parasitic peroxiredoxins, engage in functional heterooligomerization. These findings challenge the long-held paradigm of peroxiredoxin homooligomerization and reveal a novel mechanism for regulating redox homeostasis. Our study provides new insights into peroxiredoxin structural plasticity with broad implications for redox biology, stress responses, and cellular adaptation.

biochemistry↗

bioRxiv2024

A priority code in presequences: mitochondrial targeting signals assign specific import characteristics to precursor proteins

The biogenesis of mitochondria relies on the import of hundreds of different precursor proteins from the cytosol. Most of these proteins are synthesized with N-terminal presequences which serve as mitochondrial targeting signals. Presequences consistently form amphipathic helices, but they considerably differ in respect to their primary structure and length. Here we show that presequences can be classified into seven different groups based on their specific features. Using a test set of different presequences, we observed that group A presequences endow precursor proteins with improved in vitro import characteristics. We developed IQ-Compete (for Import and de-Quenching Competition assay), a novel assay based on fluorescence de-quenching, to monitor the import efficiencies of mitochondrial precursors in vivo. With this assay, we confirmed the increased import competence of group A presequences. Using mass spectrometry, we found that the presequence of the group A protein Oxa1 specifically recruits the tetratricopeptide repeat (TPR) containing protein TOMM34 to the cytosolic precursor protein. TOMM34 apparently serves as a presequence-specific targeting factor which increases the import efficiency of a specific subset of mitochondrial precursor proteins. Our results suggest that presequences contain a protein-specific priority code that encrypts the targeting mechanism of individual mitochondrial precursor proteins.

biochemistry↗

bioRxiv2023

Degradation of Fatty Acid Export Protein1 by Rhomboid-Like Protease11 Contributes to Cold Tolerance in Arabidopsis

Plants need to adapt to different stresses to optimize growth under unfavorable conditions. The abundance of the chloroplast envelope located Fatty Acid Export Protein1 (FAX1) decreases after the onset of low temperatures. However, it was unclear how FAX1 degradation occurs and whether altered FAX1 abundance contributes to cold tolerance in plants. The rapid cold-induced increase in rhomboid-like protease11 (RBL11) transcript, the physical interaction of RBL11 with FAX1, the specific FAX1 degradation after RBL11 expression, and the absence of cold-induced FAX1 degradation in rbl11 loss-of-function mutants suggest that this enzyme is responsible for FAX1 degradation. Proteomic analyses showed that rbl11 mutants have higher levels of FAX1 and other proteins involved in membrane lipid homeostasis, suggesting that RBL11 is a key element in the remodeling of membrane properties during cold. Consequently, in the cold, rbl11 mutants show a shift in lipid biosynthesis towards the eukaryotic pathway, which coincides with impaired cold tolerance. To demonstrate that cold sensitivity is due to increased FAX1 levels, FAX1 overexpressors were analyzed. rbl11 and FAX1 overexpressor mutants show superimposable phenotypic defects upon exposure to cold temperatures. Our results show that the cold-induced degradation of FAX1 by RBL11 is critical for Arabidopsis to survive cold and freezing periods. One sentence summaryDegradation of the inner envelope protein Fatty Acid Export1 via Rhomboid Like Protease11 represents a critical process to achieve cold and frost tolerance in Arabidopsis

plant biology↗

bioRxiv2023

Spliceosomal complex components are critical for adjusting the C:N balance during high-light acclimation

Plant acclimation to an ever-changing environment is decisive for growth, reproduction and survival. Light availability limits biomass production on both ends of the intensity spectrum. Therefore, the adjustment of plant metabolism is central to high-light (HL) acclimation, and accumulation of photoprotective anthocyanins is commonly observed. However, mechanisms and factors regulating the HL acclimation response are less clear. Two Arabidopsis mutants of spliceosome components exhibiting a pronounced anthocyanin overaccumulation in HL were isolated from a forward genetic screen for new factors crucial for plant acclimation. Time-resolved physiological, transcriptome and metabolome analysis revealed a vital function of the spliceosome components for rapidly adjusting gene expression and metabolism. Deficiency of INCREASED LEVEL OF POLYPLOIDY1 (ILP1), NTC-RELATED PROTEIN1 (NTR1), and PLEIOTROPIC REGULATORY LOCUS1 (PRL1) resulted in a marked overaccumulation of carbohydrates and strongly diminished amino acid biosynthesis in HL. While not generally limited in N-assimilation, ilp1, ntr1, and prl1 mutants showed higher glutamate levels and reduced amino acid biosynthesis in HL. The comprehensive analysis reveals a function of the spliceosome in the conditional regulation of the carbon:nitrogen-balance and the accumulation of anthocyanins during HL acclimation. The importance of gene expression, metabolic regulation, and re-direction of carbon towards anthocyanin biosynthesis for HL acclimation are discussed.

molecular biology↗

bioRxiv2023

DataPLAN: a web-based data management plan generator for the plant sciences

Research Data Management (RDM) is a system for the effective handling of research data that enables scientists to structure their research questions and ensure best practices throughout the data lifecycle, from acquisition, computation and annotation to data publication and re-use. Data management plans (DMPs) are documents that formally set out the RDM of a project and are required by many funding bodies. DMPs help to organize and structure RDM strategies, thus promoting data findability, accessibility, interoperability and reusability (FAIR). Although DMPs incorporate methods and standards that can be reused by different research projects, the standardization of DMP content is not as evident as the standardization of RDM practices and data/metadata. To address this issue in the plant sciences, we developed DataPLAN - a tool that combines a questionnaire with pre-written standardized responses. We wrapped the questionnaire in a serverless single-page web application that can then generate standardized responses from DMP templates. The current templates cater to plant research grant proposals for Horizon 2020, Horizon Europe and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). In the future the range of templates will be extended to accommodate other funding schemes, thereby enabling more users to generate their own templates. The DataPLAN web application is open-source and does not require an internet connection. By utilizing DataPLAN, the workload associated with creating, updating, and adhering to DMPs is significantly reduced.

plant biology↗

bioRxiv2023

Competition co-immunoprecipitation reveals interactors of the chloroplast CPN60 chaperonin machinery

The functionality of essential metabolic processes in chloroplasts depends on a balanced integration of nuclear-and chloroplast-encoded polypeptides into the plastids proteome. The chloroplast chaperonin machinery is an essential player in chloroplast protein folding with a more intricate structure and subunit composition compared to the orthologous GroEL/ES chaperonin of Escherichia coli. However, its exact role in chloroplasts remains obscure, mainly because of a very limited knowledge about the folded substrates. We employed the competition immunoprecipitation method for the identification of the chaperonins substrates in Chlamydomonas reinhardtii. Co-immunoprecipitation of the target complex in the presence of increasing amounts of isotope-labelled competitor epitope and subsequent mass spectrometry analysis specifically allowed to distinguish true interactors from unspecifically co-precipitated proteins. Besides known substrates such as RbcL, we revealed numerous new substrates with high confidence. Identified substrate proteins differ from bulk chloroplast proteins by a higher content of beta-sheets, lower alpha-helical content and increased aggregation propensity. Immunoprecipitations performed with a subunit of the co-chaperonin lid revealed the ClpP protease as a specific partner complex, with altered interactions during heat stress, pointing to a close collaboration of these machineries to maintain protein homeostasis in the chloroplast.

molecular biology↗

bioRxiv2020

The mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress

Most mitochondrial proteins are synthesized as precursors in the cytosol and post-translationally transported into mitochondria. The mitochondrial surface protein Tom70 acts at the interface of the cytosol and mitochondria. In vitro import experiments identified Tom70 as targeting receptor, particularly for hydrophobic carriers. Using in vivo methods and high content screens, we revisited the question of Tom70 function and considerably expanded the set of Tom70-dependent mitochondrial proteins. We demonstrate that the crucial activity of Tom70 is its ability to recruit cytosolic chaperones to the outer membrane. Indeed, tethering an unrelated chaperone-binding domain onto the mitochondrial surface complements most of the defects caused by Tom70 deletion. Tom70-mediated chaperone recruitment reduces the proteotoxicity of mitochondrial precursor proteins, in particular of hydrophobic inner membrane proteins. Thus, our work suggests that the predominant function of Tom70 is to tether cytosolic chaperones to the outer mitochondrial membrane, rather than to serve as a mitochondria-specifying targeting receptor.

cell biology↗

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↗

bioRxiv2019

Differential degradation of RNA species by autophagy related pathways in plants

An important function of the plant vacuole is the recycling of the delivered proteins and RNA by autophagy. We provide the first plant vacuolar small RNome by isolation of intact vacuoles from Barley and Arabidopsis, subsequent RNA purification and Next Generation Sequencing. In these vacuolar sRNomes, all types of cellular RNAs were found including those of chloroplast origin, suggesting a bulk-type of RNA transfer to, and breakdown in vacuoles. ATG5 is a major representative of autophagy genes and the vacuolar RNA composition in corresponding knockout plants differed clearly from controls as most chloroplast derived RNA species were missing. Moreover, the read length distribution of RNAs found in ATG5 mutants differed to control samples, indicating altered RNA processing. In contrast, vacuolar RNA length and composition of plants lacking the vacuolar RNase2 (rns2-2), involved in cellular RNA homeostasis, showed minor alterations, only. Our data therefore suggests that mainly autophagy components are responsible for selective transport and targeting of different RNA species into the vacuole for degradation. In addition, mature miRNAs were detected in all vacuolar preparations, however in ATG5 mutants at much lower frequency, indicating a new biological role for vacuolar miRNAs apart from becoming degraded.

plant biology↗