Biology subjects

Jansen, G.

Publications and source records attributed to Jansen, G..

8 recordsLinked to original sources

bioRxiv2024

Proximity Interactome analyses unveil novel regulators of IRE1a canonical signaling

The unfolded protein response (UPR) is a key adaptive pathway that controls endoplasmic reticulum (ER) homeostasis. The UPR is transduced by three ER-resident sensors of ER homeostasis disruption in the lumen of this compartment. They trigger select downstream signaling pathways in the cytosol and nucleus. Among them, IRE1 (referred to as IRE1 hereafter), a type I transmembrane protein, senses accumulation of improperly folded proteins in the ER lumen and transduces signals through both kinase and endoribonuclease (RNase) activities in the cytosol. IRE1 catalyzes XBP1 mRNA unconventional splicing and RNA degradation (Regulated IRE1 Dependent Decay, termed RIDD). Recent studies have reported that IRE1-dependent protein-protein interactions (PPi) drive additional non-canonical IRE1 functions. Herein, we define the IRE1 signalosome as a list of IRE1 binding partners (direct or not) which alter IRE1 signaling towards XBP1 mRNA splicing and RIDD. Here we determined the IRE1 in situ interactome using BioID, putatively connecting IRE1 to previously unrecognized cellular functions. In addition, we link the binding of several IRE1 partners to the regulation of its RNase. Furthermore, we identify HNRNPL as an IRE1-interacting partner, previously unrecognized, which stabilizes IRE1 under basal conditions by counteracting ERAD-mediated degradation. Overall, the characterization of the IRE1 signalosome not only reveals the multi-faceted control of IRE1 RNase activity and stability by its interacting partners and allow us to discuss putative additional IRE1 regulators and cellular functions based on the nature of its interactome and its localization.

biochemistry↗

bioRxiv2024

Tolerance thresholds underlie responses to DNA damage during germline development

Selfish DNA modules like transposable elements (TEs) are particularly active in the germline, the lineage that passes genetic information across generations. New TE insertions can disrupt genes and impair the functionality and viability of germ cells. However, we find that in P-M hybrid dysgenesis in Drosophila, a sterility syndrome triggered by the P-element DNA transposon, germ cells harbour unexpectedly few new TE insertions, despite accumulating DNA double-strand breaks (DSBs) and inducing cell cycle arrest. Using an engineered CRISPR-Cas9 system, we show that generating DSBs at silenced P-elements or other non-coding sequences is sufficient to induce germ cell loss independently of gene disruption. Indeed, we demonstrate that both developing and adult mitotic germ cells are sensitive to DSBs in a dosage-dependent manner. Following the mitotic-to-meiotic transition, however, germ cells become more tolerant to DSBs, completing oogenesis regardless of the accumulated genome damage. Our findings establish DNA damage tolerance thresholds as crucial safeguards of genome integrity during germline development.

developmental biology↗

bioRxiv2021

The macrophage reprogramming ability of antifolates reveals soluble CD14 as a potential biomarker for methotrexate response in rheumatoid arthritis

The physio-pathological relevance of the one-carbon metabolism (OCM) is illustrated by the chemotherapeutic and anti-inflammatory effects of the antifolates Pemetrexed (PMX) and Methotrexate (MTX) in cancer and rheumatoid arthritis (RA). We report that OCM determines the functional and gene expression profile of human macrophages. PMX induces the acquisition of a p53-dependent proinflammatory gene signature in human monocyte-derived macrophages (GM-MO). Indeed, OCM blockade reprograms GM-MO towards a state of LPS-tolerance at the signaling and functional levels, an effect abolished by folinic acid. Importantly, OCM blockade led to reduced expression of membrane-bound and soluble CD14 (sCD14), whose exogenous addition restores LPS sensitivity. The therapeutic relevance of these results was confirmed in early RA patients, as MTX-responder RA patients exhibit lower sCD14 serum levels, with baseline sCD14 levels predicting MTX response. Our results indicate that OCM is a metabolic circuit that critically mediates the acquisition of innate immune tolerance, and positions sCD14 as a valuable tool to predict MTX-response in RA patients.

immunology↗

bioRxiv2021

Plasticity in gustatory and nociceptive neurons controls decision making in C. elegans salt navigation

A conventional understanding of perception assigns sensory organs the role of capturing the environment. Better sensors result in more accurate encoding of stimuli, allowing for cognitive processing downstream. Here we show that plasticity in sensory neurons mediates a behavioral switch in C. elegans between attraction to NaCl in naive animals and avoidance of NaCl in preconditioned animals, called gustatory plasticity. Ca2+ imaging in ASE and ASH NaCl sensing neurons reveals multiple cell-autonomous and distributed circuit adaptation mechanisms. A computational model quantitatively accounts for observed behaviors and reveals roles for sensory neurons in the control and modulation of motor behaviors, decision making and navigational strategy. Sensory adaptation dynamically alters the encoding of the environment. Rather than encoding the stimulus directly, therefore, we propose that these C. elegans sensors dynamically encode a context-dependent value of the stimulus. Our results demonstrate how adaptive sensory computation can directly control an animals behavioral state.

neuroscience↗

bioRxiv2020

Mechanism of life-long maintenance of neuron identity despite molecular fluctuations

Cell fate is maintained over long timescales, yet molecular fluctuations can lead to spontaneous loss of this differentiated state. We uncovered a mechanism that explains life-long maintenance of ASE neuron fate in C. elegans by the terminal selector transcription factor CHE-1. Fluctuations in CHE-1 level are buffered by the reservoir of CHE-1 bound at its target promoters, which ensure continued che-1 expression by preferentially binding the che-1 promoter. We validated this mechanism by showing that che-1 expression was resilient to induced transient CHE-1 depletion, while both expression of CHE-1 targets and ASE function were lost. We identified a 130 bp che-1 promoter fragment responsible for this resilience, with deletion of a homeodomain binding site in this fragment causing stochastic loss of ASE identity long after its determination. Because network architectures that support this mechanism are highly conserved in cell differentiation, it may explain stable cell fate maintenance in many systems.

developmental biology↗

bioRxiv2019

Hotspot Dosages of Most Rapid Antibiotic Resistance Evolution

We treated Escherichia coli with the antibiotic erythromycin from zero to high dosages to determine how the evolutionary dynamics of antibiotic resistant phenotypes and genotypes depend on dose. The most rapid increase in resistance was observed just below erythromycins minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis of this: simultaneous selection for copy number variation in 3 resistance mechanisms which shared an inverted-U pattern of dose-dependent selection with several insertion sequences and an integron. Many genes did not conform to this pattern, however, because of changes in selection as dose increased: media adaptation at zero-to-low dosages gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux dominated at higher dosages where population densities were lowest. All dosages saw E. coli amplify the efflux operons acr and emrE at rates that correlated strongly with changes in population density that exhibited an inverted-U geometry too. However, we show by example that inverted-U geometries are not a universal feature of dose-resistance relationships.

evolutionary biology↗

bioRxiv2019

Signaling compartment at the ciliary tip is formed and maintained by intraflagellar transport and functions as sensitive salt detector

Primary cilia are ubiquitous antenna-like organelles that mediate cellular signaling and represent hotspots for human diseases termed ciliopathies. How signaling subcompartments are established within the microtubule-based organelle, and for example support Hedgehog or cGMP signal transduction pathways, remains a central question. Here we show that a C. elegans salt-sensing receptor type guanylate cyclase, GCY-22, accumulates at a high concentration within the distal region of the cilium. This receptor uses DAF-25 (Ankmy2 in mammals) to cross the transition zone (TZ) membrane diffusion barrier in the proximal-most region of the ciliary axoneme. Targeting of GCY-22 to the ciliary tip is dynamic, requiring the cargo-mobilizing intraflagellar transport (IFT) system. Disruption of transit across the TZ barrier or IFT trafficking causes GCY-22 protein mislocalization and defects in the formation, maintenance, and function of the ciliary tip compartment required for chemotaxis to low NaCl concentrations. Together, our findings reveal how a previously undescribed cilium tip cGMP signaling compartment is established and contributes to the physiological function of a primary cilium.

cell biology↗

bioRxiv2019

Expression and Purification of a Mammalian Protein: Cytosolic Domain of IRE1α from Insect Sf21 Cells

Eukaryotic proteins can be expressed in different heterologous systems. However, mammalian proteins in general have specific post-translational processing requirements that may not be fulfilled by a regular bacterial expression system. In this study, we use an insect cell system to express a mammalian protein of interest. Spodoptera frugiperda (Sf21) cells were used in conjunction with a baculoviral expression system to produce the cytosolic domain (CD) of IRE1, an endoplasmic reticulum (ER) stress sensor protein. Inositol Requiring Enzyme 1 (IRE1) is a dual function kinase and endoribonuclease protein that cleaves X-box binding protein (XBP1) mRNA. We used the pFastBac plasmid to insert the coding sequence into a recombinant bacmid shuttle vector which was then used to infect Sf21 cells. The expressed protein was then purified with an MBPTrap column to obtain >85% pure protein.

molecular biology↗