Biology subjects

Neumann, S.

Publications and source records attributed to Neumann, S..

At least 19 recordsLinked to original sources

bioRxiv2026

MassBank Human: The annotated human metabolome

Mass spectrometry-based metabolomics is essential for deciphering human metabolic functions and metabolite dark matter. However, the dark matter of the human metabolome is intricately hidden. Therefore, we developed MassBank Human, a curated library that distills 36,512,540 MS2 spectra from 76 public human datasets into 203,886 high-quality spectra via spectral averaging, recalibration, and filtering to achieve high mass accuracy. We further used three metabolite annotation tools and developed a Zipf-Bayesian rank aggregation framework to aggregate their rankings with false discovery rate control. This framework assigned molecular formulas, chemical classes, and planar structures to 55,564, 22,619, and 14,198 spectra, respectively. Approximately half of the annotated structures potentially originated from food, pollutants, or gut microbiota. In a metabolome analysis of colorectal cancer cells, MassBank Human doubled structural annotation coverage (10.6% to 21.2%), identifying acetylated polyamines as markers of metabolic rewiring. This community resource provides an annotated foundation for exploring human metabolomes.

bioinformatics↗

bioRxiv2026

mzQC: a versatile way to communicate quality information for biological mass spectrometry

Reliable quality control (QC) is essential for reproducible biological mass spectrometry, yet QC information is still typically stored in tool-specific, poorly interoperable formats that hinder comparison, reuse, and transparent reporting. We present mzQC, a community-developed standard from the HUPO Proteomics Standards Initiative for the compact, machine-readable representation of QC metrics and their associated metadata across mass spectrometry workflows. mzQC is implemented in JSON, organized to support both individual mass spectrometry acquisitions and collections thereof, with formal QC metrics definitions supported by controlled vocabularies to ensure unambiguous metric interpretation and semantic consistency. The format is supported by validation tools and reference libraries in Python, R, and Java, facilitating integration into existing software ecosystems. We demonstrate the utility of mzQC across diverse analytical modalities and QC settings, spanning longitudinal instrument monitoring, acquisition-method evaluation, study-level quality assessment, repository-scale data characterization, and spatially resolved mass spectrometry imaging. Together, these use cases show that mzQC provides not merely a file format, but a shared foundation for interoperable QC reporting, large-scale data assessment, and more rigorous, reproducible, and reusable mass spectrometry-based research.

bioinformatics↗

bioRxiv2026

The receptor kinase NILR1 confers nematode resistance through developmental rather than canonical immune signaling

O_LINILR1 contributes to quantitative resistance against Heterodera schachtii and signals through a brassinosteroid-type kinase cascade, but whether its contribution engages canonical immune signaling or follows a distinct, developmentally biased logic has remained unclear. C_LIO_LIWe profiled early transcriptional responses of wild-type and nilr1 roots to H. schachtii by RNA-seq at 30 min and 3 h post inoculation and analyzed them using a genotype x treatment interaction model, complemented by gene set enrichment and integration with cell-type-resolved, brassinosteroid-responsive regulatory networks. C_LIO_LIWe found that canonical PTI marker transcription and flg22-induced ROS production were preserved or even elevated in nilr1, indicating that the tested PTI outputs are largely maintained despite increased susceptibility. Instead, genes whose nematode-induced responses showed NILR1-sensitive interaction effects were enriched for a HAT7/GTL1 centred cortex developmental module, and genetic disruption of GTL1/DF1 moderately altered H. schachtii parasitism, consistent with a role for this module in shaping host permissiveness. C_LIO_LIOur data support a model in which NILR1 contributes to nematode resistance primarily via developmental, brassinosteroid-type signaling rather than via the canonical PTI outputs assayed here, consistent with a co-option of BRI1 clade (LRR-RLK-Xb) architecture -- a receptor family classically associated with development -- into a pathway that modulates susceptibility to a plant-parasitic nematode. C_LI

plant biology↗

bioRxiv2026

Essential Molecular Variables of liverworts in biological soil crusts

(1) In plant ecology, functional traits are widely used to predict plant performance in ecosystems. Little is known on molecular traits and how they integrate with the classical trait spectrum, in particular in non-vascular land plants. We conceptualize Essential Molecular Variables (EMVs) using complex-thallose liverworts in biocrusts as reference. (2) We combined morphometry and bioimaging with liquid chromatography high- resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition of tandem mass-spectra (DDA-MS). To identify EMVs, data mining was performed including regression trees, random forest and redundancy analysis combined with manual filtering and functional annotation using literature and chemical libraries. (3) We found the molecular trait spectrum to be highly structured and largely orthogonal to classical traits. We identified six major categories of EMVs: molecule structure, carbon metabolism, amino acids and peptides, shikimates and phenylpropanoids, terpenoids and alkaloids that were functionally related to biotic interactions and bioclimatic properties. (4) We find EMVs to be indicators that characterize plant performance in ecosystems. Molecular traits and EMVs represent the mechanistic link to form and function and extend the functional trait concept. They provide mechanistic insights into how global changes destabilize liverworts in biocrusts and represent a new tool set by informing functional ecology on molecular mechanisms.

ecology↗

bioRxiv2026

Predicted Bacterial uRBSs Reveal Translational Coupling and Ribosome Mediated RBS Occlusion as Gene-Controlling Mechanisms

Upstream open reading frames (uORFs) in the 5' leader of bacterial mRNAs can modulate gene expression, yet genome-wide identification remains limited. We combined bioinformatic prediction of ribosome-binding sites (RBSs) - a Shine-Dalgarno sequence and a start codon - with experimental validation to uncover new uORFs in Sinorhizobium meliloti 2011. From totally 1106 predicted upstream RBSs (uRBSs), we first examined 15 candidates using eGFP reporters and integrating existing RNA-seq and Ribo-seq data. Translation was detected at 13 sites, with fluorescence intensity broadly correlating with predicted initiation rates. Two uRBSs correspond to gene start sites, thereby refining gene annotations. In nine cases, uRBS mutations affected downstream gene expression in reporter fusions. Among others, the data suggests that a Type I secretion system operon, the RNA chaperone gene hfq, and metabolic genes are regulated by uORFs. Four uORFs acted through translational coupling. We also identified uRBSs that were ribosome-occupied yet (nearly) silent in eGFP assays, and closely spaced to the downstream main RBS (mRBS). These uRBSs probably mediate ribosomal occlusion downregulating lacR and SM2011_RS36230. A re-screen of the prediction set revealed 335 close uRBS/mRBS pairs. Three of them were analyzed, supporting the proposed ribosomal occlusion mechanism for SM2011_RS03630 and SM2011_RS22110, while for glnK translational coupling to an uORF was suggested. These results indicate that uORFs are more widespread in bacteria than previously recognized and suggest that direct ribosomal occlusion of the mRBS is a novel mechanism for down-regulating protein synthesis.

molecular biology↗

bioRxiv2025

Visual dependence in postural control is increased in older adults

Successful postural control depends on the integration of visual, vestibular, and proprioceptive inputs. With age, postural control degrades, leading to impaired balance and greater fall risk. Understanding how this integration changes over the lifespan is invaluable for designing more effective interventions that enable healthy postural control in older age. Earlier studies measured visual dependence using perceptual tasks or spontaneous sway comparisons across visual conditions. This study evaluates how visual dependence differs between younger and older adults within the postural control mechanism using a Central Sensorimotor Integration (CSMI) test. Eighty healthy adults (n=40, 60-87 years, n=40, 21-52 years) were exposed to small pseudorandom visual scene movements implemented in virtual reality while standing on a compliant surface. Sway responses were measured using virtual reality trackers and interpreted using an established frequency domain balance control model. Model parameters included visual weight, proportional and derivative feedback gains, time delay, and torque feedback gain. Test-retest reliability was assessed in a subgroup (n = 40) and showed excellent intra-class correlation coefficients for visual weight, proportional and derivative feedback gains (ICC = 0.89- 0.96), and lower ICCs for time delay (ICC=0.59) and torque parameters (ICC=0.39). The main difference between age groups was visual dependence, with older adults relying 40% on vision, compared to 33% for the younger group (p = 0.042). No significant group differences were found in other model parameters. Our results provide direct evidence of an increase in visual contribution to posture control with age.

neuroscience↗

bioRxiv2025

Cytoplasmic and nuclear protein interaction networks of the synapto-nuclear messenger CRTC1 in neurons reveal cooperative chromatin binding between CREB1 and CRTC1, MEF2C and RFX3

Glutamatergic stimulation of excitatory neurons triggers the synapto-nuclear translocation of the cAMP response element (CRE) binding protein (CREB) regulated transcription coactivator 1 (CRTC1), resulting in the transcription of CREB1 target genes. Whether and how CRTC1 and CREB1 interact with other transcription factors to regulate activity-dependent transcription, and what the role of CRTC1 is in neurons beyond the activation of CREB1 regulated transcription, remains unknown. To address these questions in an unbiased manner, we used proximity labeling to identify CRTC1-proximal proteins in cytoplasmic and nuclear compartments of rodent forebrain neurons. The cytoplasmic CRTC1 proxisome included a variety of signaling pathways and downstream cellular processes involved in synaptic plasticity. In contrast, the nuclear CRTC1 proxisome included transcription factors that mediate activity-dependent transcription, chromatin factors, and splicing factors. Our data revealed that CRTC1 and CREB1 interact with MEF2C and RFX3 transcription factors in an activity-dependent manner. Thus, in chromatin immunoprecipitation-sequencing experiments, CREB1 was prebound to chromatin regions containing bZIP motifs in a manner that was unchanged by neuronal activity, while glutamatergic stimulation triggered the recruitment of CRTC1 and CREB1 to activity-dependent enhancers enriched in motifs for MEF2C and RFX3. Collectively, these results not only enhance our understanding of the role of cytoplasmic and nuclear CRTC1 in neurons, but also reveal a role for CRTC1 in promoting cooperativity of CREB1 with other transcription factors in response to synaptic activity.

neuroscience↗

bioRxiv2025

Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import

Lentiviruses like HIV-1 infect non-dividing cells by traversing the nuclear pore, but studying this process has been challenging due to its scarcity and dynamic nature in infected cells. Here, we developed a robust cell-permeabilization system that recapitulates HIV-1 nuclear import and established an integrated cryo-correlative workflow combining cryo-CLEM, cryo-FIB, and cryo-ET for targeted imaging of this process. These advancements enabled the successful capture of 1,899 HIV-1 cores at various stages of nuclear import. Statistical and structural analyses of native wild-type and mutant cores revealed that HIV-1 nuclear import depends on both capsid elasticity and nuclear pore adaptability, as well as nuclear factors such as CPSF6. Brittle cores fail to enter the nuclear pore complex (NPC), while CPSF6-binding-deficient cores stall inside the NPC, resulting in impaired nuclear import. Intriguingly, nuclear pores function as selective filters favoring the import of smaller, tube-shaped cores. Our study opens new avenues for dissecting the biochemistry and structural biology of HIV-1 nuclear import as well as downstream events including core uncoating and potentially integration, with unprecedented detail.

microbiology↗

bioRxiv2024

Estimating essential phenotypic and molecular traits from integrative biodiversity data

In the context of biodiversity, only few functional traits and mechanisms are known from underrepresented groups such as mosses (bryophytes). Here, we use 16 field samples of complex thallose liverworts (order Marchantiales) collected from biological soil crusts as reference data for the reusable computational framework iESTIMATE that integrates and extracts phenotypic and molecular traits; and estimates Essential Molecular Variables (EMV). Our reference data involves (1) bioimaging, (2) metabolomics, and (3) DNA marker sequencing. These data are used to demonstrate the systematic and standardized extraction of phenotypic and molecular traits. To demonstrate the reusability of our framework, we propose naming schemes, apply Random Forest to estimate EMVs, phylogenetic dendrograms and partitioning around medoids to connect evolutionary relationships with ecological hypotheses and to document knowledge gains across domains. With this work we want to encourage the combined assessment, reuse and integration of phenotypic and molecular traits into functional ecology, biodiversity and related disciplines.

ecology↗

bioRxiv2024

ATF4 orchestrates IL-1α-induced senescence in adult neural stem cells

Adult neural stem cells (NSC) are a potential source for the regeneration of damaged tissue during neuropathological conditions, but much remains unexplored. In an attempt to study the influence of neuroinflammation on NSCs, we generated a transgenic reporter rat strain that expresses the Discosoma sp. red (DsRed) fluorophore in NSCs and subjected it to traumatic brain injury (TBI). Transcriptomic analysis of NSCs isolated from TBI revealed an enrichment of stress response genes that pertained to endoplasmic reticulum (ER) stress and integrated stress response (ISR). Downstream analysis on NSC cultures pinpointed IL-1 as a trigger of ISR in these cells. At concentration levels similar to the ones measured post-TBI in rats, IL-1 induced the translation of activating transcription factor 4 (ATF4), an ISR master regulator. Further, ATF4 was necessary for the IL-1 -dependent induction of a senescent profile in NSCs, which included a metabolic shift towards glycolysis, induction of senescence-associated secretory phenotype, SASP, and cell cycle arrest. In summary, the ISR/ATF4 pathway seems to play a major role in NSC function during neuroinflammation and provides a therapeutic tool for protecting the NSC pool during these conditions.

neuroscience↗

bioRxiv2023

Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus

Aging-related memory impairment and pathological memory disorders such as Alzheimers disease differ between males and females, and yet little is known about how aging-related changes in the transcriptome and chromatin environment differ between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus in both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response and synaptic function, and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic function. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE-1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Sex differences in gene expression and chromatin accessibility were amplified with aging, findings that may shed light on sex differences in aging-related and pathological memory loss. HighlightsO_LIAging amplifies sex differences in the transcriptome and chromatin accessibility of mouse hippocampus C_LIO_LIAging is associated with widespread changes in the transcriptome of mouse hippocampus, including in genes involved in immune response and synaptic function C_LIO_LIMyelin sheath-related genes in aged hippocampus show female-biased expression C_LIO_LIAlternative splicing of myelin sheath-related genes changes with aging in the hippocampus C_LIO_LISex-bias is evident in alternative splicing of nuclear and primary cilia genes C_LIO_LIAging in the hippocampus is associated with increased chromatin accessibility in both males and females C_LIO_LILINE-1 derived sequences are more accessible and LINE-1 transcripts are upregulated in the aged hippocampus of both males and females C_LIO_LIPromoter and CpG-rich regions show male-biased accessibility C_LI

neuroscience↗

bioRxiv2023

Leaf metabolic traits reveal hidden dimensions of plant form and function

The plant metabolome encompasses the biochemical mechanisms through which evolutionary and ecological processes shape plant form and function1,2. However, while the metabolome should thus be an important component of plant life-history variation3, we know little about how it varies across the plant kingdom. Here, we use the plant functional trait concept4 - a powerful framework for describing plant form and function5-7 - to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five discriminant metabolic functional traits reveals that plants vary along two major axes of leaf metabolic specialization - a leaf chemical defense spectrum and an expression of leaf longevity. These axes are qualitatively consistent for tropical and temperate species, with many trait combinations being viable. However, axes of leaf metabolic specialization vary orthogonally to life-history strategies described by widely used functional traits5-7, while being at least equally important to them. Our findings question classical trait6 and plant defense8 theory that predicts relationships between the leaf chemical phenotype, plant productivity, and pace of life. Moreover, we show that metabolic functional traits describe unique dimensions of plant life-history variation that are complementary to, and independent from, those captured by existing plant functional traits.

ecology↗

bioRxiv2022

A novel approach to quantifying inter-individual distance in insects

1Behaviour involving two or more individuals within the same species is known as social behaviour. Sexual dimorphisms and environmental cues as well as age, experience and social hierarchy shape social behaviour. The study of this complex behaviour, however, has one essential boundary condition: the distance between individuals. Because social signals (e.g. acoustic, visual or olfactory) have limited reach the inter-individual distance is crucial for the correct transmission of such signals. In this study we present a newly developed assay to study group behaviour and inter-individual distance in Drosophila melanogaster. This assay consists of a circular observation space flanked by two automatic release devices that allow flies to enter individually. By releasing the flies one at a time, the observer can study different features of (intra-)group behaviour with different group compositions. Importantly, the observer can control (manually or through automatisation) the increase of group size over time. Over the last decades insects became more relevant as convenient model organisms to study the neurophysiological and genetic basis of (human) neuro-developmental disorders. Drosophila models are used to study the genetic and neuronal underpinnings of a wide range of neurological disorders. In some cases the studies revealed alterations in social behaviour consistent with descriptions of behavioural symptoms in human disorders. Social behaviours in Drosophila are well-studied and include courtship, mating, aggression and group interactions. This setup will facilitate the analysis of these aspects of group interactions in Drosophila, allowing for a deeper understanding of the neuronal circuits and genetic factors involved in those behaviours. 2 Contribution to the fieldSocial behaviour pertains to the most sophisticated behavioural feats, as it involves multiple, interacting individuals. These complex interactions often conceal the underlying neuronal and ethological mechanisms. One of the most basal ethological mechanisms is the inter-individual distance, which resembles a perimeter in which each individual needs to formulate a response to the approach of others. We introduce a device that allows to test the inter-individual distance under consistent circumstances, by automating the entry time and direction of conspecifics into the arena. We can further observe the composition, dynamics and forming of larger animal groups as well as their separating. We can also observe how the individual distances alter during the process. Also other behaviours can be easily observed, e.g. aggression, courtship, homosexual courtship, etc. We successfully employed this approach in [1] and could discriminate the role of different neuroligins in social behaviour. We provide a detailed description including building plans and material lists for this social observation device. The system can be run in an automatic mode to ensure the consistency of experiments or in a manual mode to test animals under more flexible social situations. We provide multiple back lighting systems to test animals in the dark (infra-red LEDs) or in illuminated environments (vis. range LEDs). The system is fully automated and can be linked with a number of animal trackers (e.g. T-Rex, deeplabcut, LACE, etc.) via simple videography. We hope that our experimental setup augments the variety of behaviours testable in ethological setups (T-maze, water-mazes, operant conditing setups, etc) with social interaction and group formation.

animal behavior and cognition↗

bioRxiv2021

Direct imaging of anthrax intoxication in animals reveals shared and individual functions of CMG-2 and TEM-8 in cellular toxin entry

The virulence of Bacillus anthracis is linked to the secretion of anthrax lethal toxin and anthrax edema toxin. These binary toxins consist of a common cell-binding moiety, protective antigen (PA), and the enzymatic moieties, lethal factor (LF) and edema factor (EF). PA binds either of two specific cell surface receptors, capillary morphogenesis protein-2 (CMG-2) or tumor endothelial marker-8 (TEM-8), which triggers the binding, endocytosis, and cytoplasmic translocation of LF and EF. The cellular distribution of functional TEM-8 and CMG-2 receptors during anthrax toxin intoxication in animals is not fully elucidated. Herein, we describe a novel assay to image anthrax toxin intoxication in live animals, and we use the assay to visualize TEM-8- and CMG-2-dependent intoxication. Specifically, we generated a chimeric protein consisting of the N-terminal domain of LF fused to a nuclear localization signal-tagged Cre recombinase (LFn-NLS-Cre). When PA and LFn-NLS-Cre were co-administered to transgenic mice that ubiquitously express a red fluorescent protein in the absence of Cre activity and a green fluorescent protein in the presence of Cre activity, anthrax toxin intoxication could be visualized at single-cell resolution by confocal microscopy. By using this assay, we show that CMG-2 is critical for intoxication in the liver and heart, whereas TEM-8 is required for full intoxication in the kidney and spleen. Other tissues examined were largely unaffected by single deficiences in either receptor, suggesting extensive overlap in TEM-8 and CMG-2 expression. The novel assay will be useful for basic and clinical/translational studies of Bacillus anthracis infection and for identifying on- and off-targets for reengineered toxin variants in the clinical development of cancer treatments. BackgroundAssays for imaging of anthrax toxin intoxication in animals are not available. ResultsAnthrax toxin-Cre fusions combined with fluorescent Cre reporter mice enabled imaging of anthrax toxin intoxication in animals. ConclusionShared and distinct functions of toxin receptors in cellular entry were uncovered. Significance. A simple and versatile assay for anthrax toxin intoxication is described.

pathology↗

bioRxiv2020

Plot diversity differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species

O_LIPlants produce thousands of compounds, collectively called the metabolome, which mediate interactions with other organisms. The metabolome of an individual plant may change according to the number and nature of these interactions. We tested the hypothesis that tree diversity level affects the metabolome of four subtropical tree species in a biodiversity ecosystem-functioning experiment, BEF-China. We postulated that the chemical diversity of leaves, roots and root exudates increases with tree diversity. We expected the strength of this diversity effect to differ among leaf, root and root exudates samples. Considering their role in plant competition, we expected to find the strongest effects in root exudates. C_LIO_LIIn an ecometabolomics approach, roots, root exudates and leaves of four tree species (Cinnamomum camphora, Cyclobalanopsis glauca, Daphniphyllum oldhamii, Schima superba) were sampled from selected plots in BEF-China. Samples were extracted and analysed using Liquid Chromatography-Time of Flight-Mass Spectrometry. The exudate metabolomes were normalized over their non-purgeable organic carbon level. Multivariate analyses were applied to identify the effect of both neighbouring (local) trees and plot diversity on tree metabolomes. The species and sample specific metabolites were assigned to major compound classes using the ClassyFire tool, whereas m/z features related to diversity effects were annotated manually. C_LIO_LIIndividual tree species showed distinct leaf, root and root exudate metabolomes. The main compound class in leaves were the flavonoids, whereas carboxylic acids, prenol lipids and specific alkaloids were most prominent in root exudates and roots. Overall plot diversity had a stronger effect on metabolome profiles than the diversity of local, directly neighbouring trees. Leaf metabolomes responded more often to tree diversity level than exudates, whereas root metabolomes varied the least. We found not overall correlation between metabolite richness or diversity and tree diversity. C_LIO_LISynthesis: Classification of metabolites supported initial ecological interpretation of differences among species and organs. Particularly the metabolomes of leaves and root exudates respond to differences in tree diversity. These responses were neither linear nor uniform and individual metabolites showed different dynamics. More controlled interaction experiments are needed to dissect the causes and consequences of the observed shifts in plant metabolomes. C_LI

ecology↗

bioRxiv2020

Parallelized manipulation of adherent living cells by magnetic nanoparticles-mediated forces

The remote actuation of cellular processes such as migration or neuronal outgrowth is a challenge for future therapeutic applications in regenerative medicine. Among the different methods that have been proposed, the use of magnetic nanoparticles appears to be promising since magnetic fields can act at a distance without interactions with the surrounding biological system. To control biological processes at a subcellular spatial resolution, magnetic nanoparticles can be used either to induce biochemical reactions locally or to apply forces on different elements of the cell. Here, we show that cell migration and neurite outgrowth can be directed by the forces produced by a switchable parallelized array of micro-magnetic pillars, following passive uptake of nanoparticles. Using live cell imaging, we first demonstrate that adherent cell migration can be biased toward magnetic pillars and that cells can be reversibly trapped onto these pillars. Second, using differentiated neuronal cells we were able to induce events of neurite outgrowth in the direction of the pillars without impending cell viability. Our results show that the range of forces applied needs to be adapted precisely to the cellular process under consideration. We propose that cellular actuation is the result of the force on the plasma membrane caused by magnetically filled endo-compartments, which exert a pulling force on the cell periphery.

bioengineering↗

bioRxiv2020

Interactive MS/MS Visualization with the Metabolomics Spectrum Resolver Web Service

The growth of online mass spectrometry metabolomics resources, including data repositories, spectral library databases, and online analysis platforms has created an environment of online/web accessibility. Here, we introduce the Metabolomics Spectrum Resolver (https://metabolomics-usi.ucsd.edu/), a tool that builds upon these exciting developments to allow for consistent data export (in human and machine-readable forms) and publication-ready visualisations of tandem mass spectrometry spectra. This tool supports the Human Proteome Organization - Proteomics Standards Initiatives Universal Spectrum Identifier (USI) specification, which has been extended to deal with the metabolomics use cases. To date, this resource already supports data formats from GNPS, MassBank, MS2LDA, MassIVE, MetaboLights, and Metabolomics Workbench and is integrated into several of these resources.

bioinformatics↗

bioRxiv2020

Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity

Proteome remodeling is a fundamental adaptive response and proteins in complex and functionally related proteins are often co-expressed. Using a deep sampling strategy we define Arabidopsis thaliana tissue core proteomes at around 10,000 proteins per tissue and absolutely quantify (copy numbers per cell) nearly 16,000 proteins throughout the plant lifecycle. A proteome wide survey of global post translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue and age specific roles of entire signaling modules regulating transcription in photosynthesis, seed development and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of Cysteine-rich Receptor-like Kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were co-expressed tissue and age specifically indicating functional promiscuity in the assembly of these little described protein complexes in Arabidopsis. Treatment of seedlings with flg22 for 16 hours allowed us to characterize proteome architecture in basal immunity in detail. The results were complemented with parallel reaction monitoring (PRM) targeted proteomics, phytohormone, amino acid and transcript measurements. We obtained strong evidence of suppression of jasmonate (JA) and JA-Ile levels by deconjugation and hydroxylation via IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2) under the control of JASMONATE INSENSITIVE 1 (MYC2). This previously unknown regulatory switch is another part of the puzzle of the as yet understudied role of JA in pattern triggered immunity. The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community.

plant biology↗