Biology subjects

Ziegler, J.

Publications and source records attributed to Ziegler, J..

13 recordsLinked to original sources

bioRxiv2025

Persistent CD4+ T cell functional deficits during recovery from prolonged symptomatic SARS-CoV-2 infection

Symptoms of acute SARS-CoV-2 infection often resolve quickly but are sometimes associated with persistent immune dysfunction. The factors that predispose individuals to compromised immune function have not been well defined. We investigated CD4+ T cell phenotype and function in a small cohort of individuals who recovered from mild to moderate SARS-CoV-2 infection without hospitalization and were divided into short or prolonged symptom duration groups. Five individuals with prolonged symptom duration showed marked downregulation of CD4 on CD3+CD8- T cells (CD4low group) and a poor response to TCR stimulation with the superantigen Staphylococcal enterotoxin B (SEB), as shown by weak upregulation of the activation markers CD134 and CD69. CD4 surface intensities recovered to normal levels in four of these individuals within 3-12 months. Selected cytokines (IL-1RA, IL-7, and VEGF) were elevated in individuals with low CD4, but plasma levels of anti-S1 IgG did not correlate with CD4 defects. Bulk RNA sequencing of unstimulated and SEB-treated CD3+CD8- T cells revealed a >50% reduction in the number of differentially expressed genes in the CD4low group compared to the same individuals after CD4 levels were recovered and a healthy control group. Upstream regulator analysis of differentially expressed genes in unstimulated CD4low cells suggested a response to IFN, while SEB-stimulated CD4low cells showed reduced functionality of IL-2, CD28, and SATB1 regulated pathways. In summary, prolonged symptomatic recovery from SARS-CoV-2 infection was associated with a global CD4+ T cell response defect, defined by low surface CD4 expression, evidence of IFN signaling, and defective T cell activation.

immunology↗

bioRxiv2025

Evolutionary Trade-off Between Stomatal Defense and Gas Exchange in Brassicaceae

Stomatal opening is crucial for gas exchange, but it unavoidably offers invasion by pathogens. In response, plants close stomata to prevent pathogen entry, while the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) produces coronatine (COR), a jasmonate (JA) mimic, to counteract this plant response. Here, we demonstrate that by COR, Pto exploits CYP707A1 activation in Arabidopsis thaliana, encoding an enzyme that degrades abscisic acid, essential for stomatal closure. Notably, COR-induction of CYP707A1 is absent in other Brassicaceae species, such as Capsella rubella and Eutrema salsugineum, rendering them resistant to Pto invasion. In contrast, in A. thaliana, CYP707A1 enables rapid stomatal opening at dawn in a JA-dependent manner, enhancing gas exchange and chlorophyll content, unlike C. rubella and E. salsugineum. Promoter-swap experiments confirm that the regulatory region of CYP707A1 underlies these evolutionary diversifications. Together, our study presents a mechanism underlying an evolutionary trade-off between stomatal defense and gas exchange.

plant biology↗

bioRxiv2024

A key residue of the extracellular gate provides quality control contributing to ABCG substrate specificity

For G-type ATP-binding cassette (ABC) transporters, a hydrophobic "di-leucine motif" as part of a hydrophobic extracellular gate has been described to separate a large substrate-binding cavity from a smaller upper cavity and proposed to act as a valve controlling drug extrusion. Here, we show that an L704F mutation in the hydrophobic extracellular gate of Arabidopsis ABCG36/PDR8/PEN3 uncouples the export of the auxin precursor indole-3-butyric acid (IBA) from that of the defense compound camalexin (CLX). Molecular dynamics simulations reveal an increase in free energy and pulling forces for CLX at both the entrance and exit sites of ABCG36L704F, respectively, providing a mechanistic rationale for the transport discrimination of CLX. Mutagenesis of L704 to tyrosine allows export of structurally related non-ABCG36 substrates, indole-3-acetic acid (IAA) and indole, suggesting an allosteric communication between the extracellular gate and the central substrate binding pocket. In summary, our work supports the conclusion that L704 is a key residue of the extracellular gate that provides a final quality control contributing to ABCG substrate specificity.

biochemistry↗

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

The plant specific cohesin subunit SYN4 contributes to 3D genome organization and activity

O_LIChromatin architecture in the cells of animals and fungi influences gene expression. The molecular factors that influence higher genome architecture in plants and their effects on gene expression remain unknown. Cohesin complexes, conserved in eukaryotes, are essential factors in genome structuring. Here, we investigated the relevance of the plant-specific somatic cohesin subunit SYN4 for chromatin organisation in Arabidopsis thaliana. C_LIO_LIPlants mutated in SYN4 were studied using HRM, Hi-C, RNA sequencing, untargeted and targeted metabolomics and physiological assays to understand the role of this plant-specific cohesin. C_LIO_LIWe show that syn4 mutants exhibit altered intra- and interchromosomal interactions, expressed as sharply reduced contacts between telomeres and chromosome arms but not between centromeres, and differences in the placement and number of topologically associated domains (TADs)-like structures. By transcriptome sequencing, we also show that syn4 mutants have altered gene expression, including numerous genes that control abiotic stress responses. C_LIO_LIThe response to drought stress in Arabidopsis is strongly influenced by the genome structure in syn4 mutants, potentially due to altered expression of CYP707A3, an ABA 8-hydroxylase. C_LI In briefThe 3D architecture of the genome extensively influences gene expression in animals and fungi. We show that the plant-specific cohesin subunit SYN4 affects intra- and interchromosomal interactions including telomere clustering, with consequences for the expression of genes of transient and induced biological pathways and the biosynthesis of bioactive compounds. Highly condensed genome structures at the CYP707A3 locus positively affects the stress response to water deprivation regulated by abscisic acid.

genetics↗

bioRxiv2023

Peptidoglycan from Bacillus anthracis Inhibits Human Macrophage Efferocytosis in Part by Reducing Cell Surface Expression of MERTK and TIM-3

Bacillus anthracis peptidoglycan (PGN) is a major component of the bacterial cell wall and a key pathogen-associated molecular pattern (PAMP) contributing to anthrax pathology, including organ dysfunction and coagulopathy. Increases in apoptotic lymphocytes are a late-stage feature of anthrax and sepsis, suggesting there is a defect in apoptotic clearance. Here, we tested the hypothesis that B. anthracis PGN inhibits the capacity of human monocyte-derived macrophages (M{Phi}) to efferocytose apoptotic cells. Exposure of CD163+CD206+ M{Phi} to PGN for 24h impaired efferocytosis in a manner dependent on human serum opsonins but independent of complement component C3. PGN treatment reduced cell surface expression of the pro-efferocytic signaling receptors MERTK, TYRO3, AXL, integrin V{beta}5, CD36 and TIM-3, whereas TIM-1, V{beta}3, CD300b, CD300f, STABILIN-1 and STABILIN-2 were unaffected. ADAM17 is a major membrane-bound protease implicated in mediating efferocytotic receptor cleavage. We found multiple ADAM17-mediated substrates increased in PGN-treated supernatant suggesting involvement of membrane-bound proteases. ADAM17 inhibitors TAPI-0 and Marimastat prevented TNF release, indicating effective protease inhibition, and modestly increased cell-surface levels of MerTK and TIM-3 but only partially restored efferocytic capacity by PGN-treated M{Phi}. We conclude that human serum factors are required for optimal recognition of PGN by human M{Phi} and that B. anthracis PGN inhibits efferocytosis in part by reducing cell surface expression of MERTK and TIM-3.

immunology↗

bioRxiv2023

Changes in Protein Turn-over Rates Regulate Tryptophan and Glucosinolate Biosynthesis, IAA Transport and Photosynthesis in Arabidopsis Growth and Defense Transitions

An organism continuously experiences shifts in biological states necessitating extensive rearrangement of physiology and molecular order of the cell. Here we model transitions between optimal growth conditions (homeostasis), fully induced pattern triggered immunity (PTI) and back in Arabidopsis thaliana, chronologically measuring changes in protein synthesis and degradation rates, transcript, protein and phytohormone abundance of 99 targets using qPCR and LC-MS parallel reaction monitoring (PRM). Temporally changing synthesis and degradation rates were primary determinants of abundance, next to changes in mRNA levels, of tryptophan, glucosinolate (GS) biosynthesis and photosynthesis associated (PAP) proteins particularly in the earlier establisher phases but also in fully induced PTI. While transcripts returned to growth levels 3 to 16 hours post elicitation, protein levels remained at fully induced PTI levels up to 16 hours into the transitory phase back to optimal growth. A notable exception were polar auxin transporters PIN3 and PIN7 levels which decreased in PTI but quickly returned to initial homeostasis levels after transition, although global auxin levels only decreased by 20%. Tryptophan, GS and JA biosynthesis proteins all increased in abundance in the wild type and the myc234 mutant background linking induction of the tryptophan and GS biosynthesis pathways to flg22 treatment and PTI independent of MYC2 and homologs. PAPs abundance was depleted in fully induced PTI however not in the myc234 mutant linking this active immune response to these bHLH transcription factors. FERREDOXIN-NADP(+)-OXIDOREDUCTASE (FNR1) synthesis rates decreased while its degradation rate increased in the earlier PTI establisher phase. FNR1 is the penultimate protein in the photosynthetic electron transfer chain and imparts electrons onto NADP+ however in its absence electrons are used for oxygen photoreduction and H2O2 production, an active defense compound. Thus FNR1 may be a molecular switch that switches photosystem activity between growth and defense under post-transcriptional control. The myc234 mutation generally led to delayed changes in transcript and protein abundance and also abolished IAA depletion. Protein turn-over rates of a set of PAPs were affected in the mutant suggesting a possible positive role of the transcription factors in controlling post-transcriptional regulatory processes in PTI induction.

plant biology↗

bioRxiv2022

Advected percolation in the actomyosin cortex drives amoeboid cell motility

Spontaneous locomotion is a common feature of most metazoan cells, generally attributed to the fundamental properties of the actomyosin network. This force-producing machinery has been studied down to the most minute molecular details, especially in lamellipodium-driven migration. Nevertheless, how actomyosin networks work inside contraction-driven amoeboid cells still lacks unifying principles. Here, using stable motile blebs as a model amoeboid motile system, we image the dynamics of the actin cortex at the single filament level and reveal the co-existence of three phases of the actin network with distinct rheological properties. Physical modelling shows that these three phases organize spontaneously due to a rigidity percolation transition combined with an active advection of the percolated network. This spontaneous spatial organization of the mechanical properties of the actin network, which we propose to call advected percolation, constitutes a minimal and generic locomotion mechanism. It explains, down to the single actin filament level and up to the scale of the entire cell, how amoeboid cells can propel efficiently through complex 3D environments, a feature shared by immune and cancer cells.

biophysics↗

bioRxiv2021

Bacterial-type plant ferroxidases tune local phosphate sensing in root development

Fluctuating bioavailability of inorganic phosphate (Pi), often caused by complex Pi-metal interactions, guide root tip growth and root system architecture for maximizing the foraged soil volume. Two interacting genes in Arabidopsis thaliana, PDR2 (P5-type ATPase) and LPR1 (multicopper oxidase), are central to external Pi monitoring by root tips, which is modified by iron (Fe) co-occurrence. Upon Pi deficiency, the PDR2-LPR1 module facilitates cell type-specific Fe accumulation and cell wall modifications in root meristems, inhibiting intercellular communication and thus root growth. LPR1 executes local Pi sensing, whereas PDR2 restricts LPR1 function. We show that native LPR1 displays specific ferroxidase activity and requires a conserved acidic triad motif for high-affinity Fe2+ binding and root growth inhibition under limiting Pi. Our data indicate that substrate availability tunes LPR1 function and implicate PDR2 in maintaining Fe homeostasis. LPR1 represents the prototype of an ancient ferroxidase family, which evolved very early upon bacterial colonization of land. During plant terrestrialization, horizontal gene transfer transmitted LPR1-type ferroxidase from soil bacteria to the common ancestor of Zygnematophyceae algae and embryophytes, a hypothesis supported by homology modeling, phylogenomics, and activity assays of bacterial LPR1-type multicopper oxidases.

plant biology↗

bioRxiv2020

Microbiota-root-shoot axis modulation by MYC2 favours Arabidopsis growth over defence under suboptimal light

Bidirectional root-shoot signalling is likely key in orchestrating stress responses and ensuring plant survival. Here we show that Arabidopsis thaliana responses to microbial root commensals and light are interconnected along a microbiota-root-shoot axis. Microbiota and light manipulation experiments in a gnotobiotic system reveal that low photosynthetically active radiation (LP) perceived by leaves induce long-distance modulation of root bacterial, but not fungal or oomycetal communities. Reciprocally, bacterial root commensals and particularly Pseudomomas isolates are necessary for rescuing plant growth under LP. RNA-Seq, combined with leaf inoculation experiments with biotrophic and necrotrophic microbial pathogens indicate that microbiota-induced growth under LP coincides with transcriptional repression of immune responses, thereby increasing susceptibility to both pathogens. Inspection of a set of A. thaliana mutants demonstrates that orchestration of this light-dependent growth-defence trade-off requires the transcriptional regulator MYC2. Our work indicates that aboveground stress responses in plants can be governed by signals from microbial root commensals.

plant biology↗

bioRxiv2020

MiMSI - a deep multiple instance learning framework improves microsatellite instability detection from tumor next-generation sequencing

Microsatellite instability (MSI) is a critical phenotype of cancer genomes and an FDA-recognized biomarker that can guide treatment with immune checkpoint inhibitors. Recent work has demonstrated that next-generation sequencing data can be used to identify samples with MSI-high phenotype. However, low tumor purity, as frequently observed in routine clinical samples, poses a challenge to the sensitivity of existing algorithms. To overcome this critical issue, we developed MiMSI, an MSI classifier based on deep neural networks and trained using a dataset that included low tumor purity MSI cases in a multiple instance learning framework. On a challenging yet representative set of cases, MiMSI showed higher sensitivity (0.940) and auROC (0.988) than MSISensor(sensitivity: 0.57; auROC: 0.911), an open-source software previously validated for clinical use at our institution using MSK-IMPACT large panel targeted NGS data.

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↗

bioRxiv2019

Cortical anchoring of the microtubule cytoskeleton is essential for neuron polarity and functioning

Neurons are among the most highly polarized cell types. They possess structurally and functionally different processes, axon and dendrites, to mediate information flow through the nervous system. Although it is well known that the microtubule cytoskeleton has a central role in establishing neuronal polarity, how its specific organization is established and maintained is little understood.\n\nUsing the in vivo model system Caenorhabditis elegans, we found that the highly conserved UNC-119 protein provides a link between the membrane-associated Ankyrin (UNC-44) and the microtubule-associated CRMP (UNC-33). Together they form a periodic membrane-associated complex that anchors axonal and dendritic microtubule bundles to the cell cortex. This anchoring is critical to maintain microtubule organization by opposing kinesin-1 powered microtubule sliding. Disturbing this molecular complex alters neuronal polarity and causes strong developmental defects of the nervous system leading to severely paralyzed animals.

cell biology↗