Biology subjects

Grossmann, G.

Publications and source records attributed to Grossmann, G..

13 recordsLinked to original sources

bioRxiv2026

A calcium-fingerprint atlas infers the signaling modes of complex elicitors and reveals a salt-like response to a humic biostimulant

A central challenge in plant signaling is to infer, from an observed response, the mechanism that produced it, including perception and signaling components involved. Cytosolic calcium (Ca2+) is well suited to this reverse-engineering problem: it is a universal early messenger whose spatiotemporal pattern, the Ca2+ signature, is shaped by the specific channels and receptors a stimulus activates. We hypothesize that multiparametric analysis of Ca2+ signals can identify the main signaling pathways activated by complex or poorly defined elicitors such as biostimulants. Here, we establish a quantitative framework to resolve Ca2+ dynamics in roots of Arabidopsis seedlings by transforming spatiotemporal Ca2+ transients into multidimensional signatures. Using a normalization and feature extraction approach (Crestline), we define descriptors capturing the onset time, location along the root axis, duration, and propagation of Ca2+ signals tip- or shootwards, enabling robust comparison across stimuli. Integration of these descriptors reveals stimulus-specific "calcium fingerprints" that allow systematic classification of responses to biotic and abiotic cues within a structured signaling space. To test whether projecting an uncharacterized input into this space can predict its signaling mode, we analyzed a complex humic biostimulant. Its response fell within the fast-onset region of signaling space shared by DAMP and salt responses, clearly apart from MAMP responses, and was altered in moca1, a mutant impaired in salt sensing. Together, these findings establish Ca2+ dynamics as an interpretable encoding layer for environmental information and provide a scalable framework to resolve complex biological inputs.

plant biology↗

bioRxiv2026

A membrane-anchored inhibitor of papain-like cysteine proteases promotes Pseudomonas root colonization

Pseudomonas species, spanning both beneficial and pathogenic lifestyles, possess conserved mechanisms to modulate plant immunity. Nevertheless, the mechanisms by which commensal bacteria establish and maintain host colonization remain poorly understood. Here, we report the characterization of a Pseudomonas chagasin-like protease inhibitor (Cpi1), conserved across pseudomonads representing a novel class of membrane-anchored PLCP inhibitor. Unlike previously described secreted protease inhibitors, P. putida Cpi1 is a lipoprotein localized to the bacterial surface and outer membrane vesicles (OMVs), positioning it to selectively inhibit immune-related papain-like cysteine proteases (PLCPs) during host interactions. Functional assays demonstrated inhibition of maize PLCP activity in the nanomolar range, while cpi1 deletion and chagasin motif mutants exhibited significantly impaired early root colonization, particularly in the meristematic and elongation zones. Besides, lack of cpi1 resulted in an altered structure of a maize root-associated synthetic community. We hypothesize that, Cpi1 may protect critical bacterial surface proteins from cleavage by inhibiting plant proteases and thereby modulate the release of MAMPs, dampening host immune responses. Moreover, the release of Cpi1 via OMVs could further extend its function within the root periphery and the apoplast. Together, our results uncover a conserved, membrane-anchored mechanism among pseudomonads for subverting plant immunity and establishing host-microbe interactions.

microbiology↗

bioRxiv2026

ATPLyzer An advanced ratiometric multi-colour biosensor for long-term monitoring of ATP dynamics

Adenosine triphosphate (ATP) is a central molecule in cellular metabolism, serving as the primary energy currency that links catabolic and anabolic pathways. Monitoring intracellular ATP in vivo is essential for understanding the dynamics of metabolic states, as well as intracellular functions and intercellular interactions in health and disease. We report the design and application of ATPLyzer, a series of genetically encoded, ratiometric biosensors for the monitoring of ATP levels in living cells. The matryoshka design consists of an ATP-binding cassette linked to a circularly permutated GFP coupled with an internal large stokes shift reference fluorophore, allowing for single-wavelength excitation and ratiometric output. This design overcomes limitations of conventional biosensors, reliance on dual excitation wavelengths, and susceptibility to photobleaching. Multi-colour ATPLyzer variants with different dissociation constants were characterized in vitro, exhibiting high specificity for ATP over ADP. Monitoring ATP in Escherichia coli confirmed in vivo utility and revealed growth-phase and carbon-supply-dependent ATP dynamics. The ATPLyzer biosensor offers a robust and tuneable tool for minimally invasive, time-resolved monitoring of intracellular ATP dynamics.

bioengineering↗

bioRxiv2025

Salicylic acid-induced alkalinization of the apoplast requires TRANSMEMBRANE KINASE 1 and results in growth attenuation

The phytohormone salicylic acid (SA) has a key role in regulating plant growth and stress response. In the past, most of the growth-related SA functions have been explained by crosstalk with the master growth regulator auxin. By affecting polarity of auxin transporters, SA changes auxin distribution in the root and inhibits growth of the main root and activates lateral root formation. However, only recently there is evidence emerging that SA impacts growth processes independently of nuclear auxin signalling, possessing yet unknown mechanistic functions. Here we show that SA activity depends on TRANSMEMBRANE KINASE 1 (TMK1) resulting in apoplast alkalinization and growth restriction. SA treatment prevents phosphorylation and activation of plasma membrane (PM) H+-ATPases at the cell surface and does not depend on the auxin receptor Auxin Binding Protein 1 (ABP1). We suggest that alkalinization of the apoplast by SA serves as mechanism to balance stress response and growth.

plant biology↗

bioRxiv2025

Phage biocontrol reduces the burden on plant immunity through suppression of bacterial virulence

Bacteriophages are increasingly recognized as key players in modulating plant-microbe interactions, including their potential in the biocontrol of plant pathogenic bacteria. In this study, we investigated the tripartite interaction between Arabidopsis thaliana, the bacterial plant pathogen Xanthomonas campestris pv. campestris (Xcc), and the lytic phage Seregon. Using parallel transcriptomic profiling, we characterized host and pathogen responses during infection and phage treatment. While treatment with phage Seregon did not lead to the eradication of Xcc, it significantly mitigated Xcc-induced disease symptoms, restoring leaf area to levels comparable to the uninfected control within 14 days post-inoculation. Our data revealed that phage-mediated protection is associated with early bacterial recognition, and suppression of Jasmonate (JA)-related responses in the host. Analysis of nuclear localized reporter plant lines further confirmed a significant reduction in ROS levels and JA biosynthesis in phage-treated plants. Concurrently, Xcc exhibited significant transcriptional downregulation of key virulence factors in the presence of the phage, including the genes encoding the type III secretion system, its associated effectors, and components involved in flagella biosynthesis. Remarkably, phage treatment did not lead to a significant increase in bacterial resistance to phage infection, which is in stark contrast to in vitro conditions. Taken together, this study provides first mechanistic insight into how phages can be harnessed to shape plant-pathogen interactions and highlights their potential role in enhancing plant resilience through targeted modulation of both host immunity and pathogen behavior.

microbiology↗

bioRxiv2024

Visible neural networks for multi-omics integration: a critical review

Biomarker discovery and drug response prediction is central to personalized medicine, driving demand for predictive models that also offer biological insights. Biologically informed neural networks (BINNs), also known as visible neural networks (VNNs), have recently emerged as a solution to this goal. BINNs or VNNs are neural networks whose inter-layer connections are constrained based on prior knowledge from gene on-tologies pathway databases. These sparse models enhance interpretability by embedding prior knowledge into their architecture, ideally reducing the space of learnable functions to those that are biologically meaningful. In this systematic review--the first of its kind-- we identify 86 recent papers implementing such models and highlight key trends in architectural design decisions, data sources and methods for evaluation. Growth in popularity of the approach is apparently mitigated by a lack of standardized terminology, tools and benchmarks.

bioinformatics↗

bioRxiv2024

GRIP: physics-informed neural network for gradient retention time prediction in liquid chromatography

Gradient liquid chromatography has numerous applications in life sciences. Retention time prediction remains challenging due to complex underlying physical processes and highly variable chromatographic conditions. Here, we present GRIP, a physics-informed neural network for gradient retention time prediction that explicitly uses experimental setup parameters. GRIP demonstrates zero-shot generalization to unseen chromatographic systems while being on par or out-performing the transfer learning-based baseline. This approach can computationally guide the experimental setup configuration tailored to specific compounds of interest.

bioinformatics↗

bioRxiv2022

The AUX1-AFB1-CNGC14 module establishes longitudinal root surface pH profile

Plant roots navigate in the soil environments following the gravity vector. Cell divisions in the meristem and rapid cell growth in the elongation zone propel the root tips through the soil. Actively elongating cells acidify their apoplast to enable cell wall extension by the activity of plasma membrane AHA H+-ATPases. The phytohormone auxin, central regulator of gravitropic response and root development, inhibits root cell growth, likely by rising the pH of the apoplast. However, the role of auxin in the regulation of the apoplastic pH gradient along the root tip is unclear. Here we show, by using an improved method for visualization and quantification of root surface pH, that the Arabidopsis thaliana root surface pH shows distinct acidic and alkaline zones, which are not primarily determined by the activity of AHA H+-ATPases. Instead, the distinct domain of alkaline pH in the root transition zone is controlled by a rapid auxin response module, consisting of the AUX1 auxin influx carrier, the AFB1 auxin co-receptor and the CNCG14 calcium channel. We demonstrate that the rapid auxin response pathway is required for an efficient navigation of the root tip.

plant biology↗

bioRxiv2022

The complex octoploid Craterostigma genome and tissue-specific mechanisms underlying desiccation tolerance

Resurrection plants can survive prolonged anhydrobiosis, and desiccation tolerance has evolved recurrently across land plants as a common adaptation for survival in regions with seasonal drying. Craterostigma plantagineum was among the first model resurrection plants, and many of the genetic mechanisms underlying desiccation tolerance were discovered in this important system. Here, we analyzed the complex, octoploid Craterostigma (C. plantagineum) genome and surveyed spatial and temporal expression dynamics to identify genetic elements underlying desiccation tolerance. Homeologous genes within the Craterostigma genome have divergent expression profiles, suggesting the subgenomes contribute differently to desiccation tolerance traits. The Craterostigma genome contains almost 200 tandemly duplicated early light induced proteins (ELIPs), a hallmark trait of desiccation tolerance, with massive upregulation under water deficit. We identified a core network of desiccation responsive genes across all tissues but observed almost entirely unique expression dynamics in each tissue during recovery. Roots and leaves have differential responses related to light and photoprotection, autophagy, and nutrient transport, reflecting their divergent functions. Our findings highlight a universal set of likely ancestral desiccation tolerance mechanisms to protect cellular macromolecules under anhydrobiosis, with secondary adaptations related to tissue function.

plant biology↗

bioRxiv2021

Nanodomain-mediated lateral sorting drives polarization of the small GTPase ROP2 in the plasma membrane of root hair cells

Formation of root hairs involves the targeted recruitment of the cellular growth machinery to the root hair initiation domain (RHID), a specialized site at the plasma membrane (PM) of trichoblast cells. Early determinants in RHID establishment are small GTPases of the Rho-of-plants (ROP) protein family, which are required for polarization of downstream effectors, membrane modification and targeted secretion during tip growth. It remains, however, not fully understood how ROP GTPases themselves are polarized. To investigate the mechanism underlying ROP2 recruitment, we employed Variable Angle Epifluorescence Microscopy (VAEM) and exploited mCitrine fluorophore blinking for single molecule localization, particle tracking and super-resolved imaging of the trichoblast plasma membrane. We observed the association of mCit-ROP2 within distinct membrane nanodomains, whose polar occurrence at the RHID was dependent on the presence of the RopGEF GEF3, and found a gradual, localized decrease of mCit-ROP2 protein mobility that preceded polarization. We provide evidence for a step-wise model of ROP2 polarization that involves (i) an initial non-polar recruitment to the plasma membrane via interactions with anionic phospholipids, (ii) ROP2 assembly into membrane nanodomains independent of nucleotide-binding state and, sub-sequently, (iii) lateral sorting into the RHID, driven by GEF3-mediated localized reduction of ROP2 mobility.

cell biology↗

bioRxiv2021

Strigo-D2 - a bio-sensor for monitoring the spatio-temporal pattern of strigolactone signaling in intact plants

Strigolactones (SLs) are a class of plant hormones modulating developmental programs in response to endogenous and exogenous stimuli and mediating biotic interactions. However, a comprehensive view on the spatio-temporal pattern of SL signaling has not been established and tools for a systematic in planta analysis do not exist. Here, we present Strigo-D2, a genetically encoded ratiometric SL signaling sensor, allowing the examination of SL signaling distribution with cellular resolution and its rapid response to altered SL levels in intact plants. By monitoring the abundance of a truncated and fluorescently labeled SUPPRESSOR OF MAX2 1-LIKE 6 (SMXL6) protein, a proteolytic target of the SL signaling machinery, we show that all cell types investigated have the capacity to respond to changes in SL levels but with very different dynamics. In particular, SL signaling is pronounced in vascular cells but low in guard cells and the meristematic region of the root. We also show that other hormones leave Strigo-D2 activity unchanged indicating that initial SL signaling steps work in isolation from other hormonal signaling pathways. Specificity and spatio-temporal resolution of Strigo-D2 underline the value of the sensor for monitoring SL signaling in a broad range of biological contexts and with highly instructive analytical depth.

plant biology↗

bioRxiv2019

Distinct ROPGEFs successively drive polarization and outgrowth of root hairs

Root hairs are tubular protrusions of the root epidermis that significantly enlarge the exploitable soil volume in the rhizosphere. Trichoblasts, the cell type responsible for root hair formation, switch from cell elongation to tip growth through polarization of the growth machinery to a pre-defined root hair initiation domain (RHID) at the plasma membrane. The emergence of this polar domain resembles the establishment of cell polarity in other eukaryotic systems [1-3]. Rho-type GTPases of plants (ROPs) are among the first molecular determinants of the RHID [4, 5] and later play a central role in polar growth [6]. Numerous studies have elucidated mechanisms that position the RHID in the cell [7-9] or regulate ROP activity [10-18]. The molecular players that target ROPs to the RHID and initiate outgrowth, however, have not been identified. We dissected the timing of the growth machinery assembly in polarizing hair cells and found that positioning of molecular players and outgrowth are temporally separate processes that are each controlled by specific ROP guanine nucleotide exchange factor (GEFs). A functional analysis of trichoblast-specific GEFs revealed GEF3 to be required for normal ROP polarization and thus efficient root hair emergence, while GEF4 predominantly regulates subsequent tip growth. Ectopic expression of GEF3 induced the formation of spatially confined, ROP-recruiting domains in other cell types, demonstrating the role of GEF3 to serve as a membrane landmark during cell polarization. Our findings suggest that morphogenetic programs in plants employ distinct regulatory modules for the alignment and activation of the cellular growth machinery.

cell biology↗

bioRxiv2017

An organ-on-a-chip approach for investigating root-environment interactions in heterogeneous conditions

Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip (dfRootChip), a microfluidic organ-on-a-chip platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from root guidance, monitoring of physiology and development under asymmetric conditions, tracing molecular uptake and selective drug treatments to local inoculation with microbes. We measured calcium responses in roots treated with biotic and abiotic elicitors and observed elicitor-specific signal propagation across the root from treated to untreated cells. We provide evidence for non-autonomous positive regulation of hair growth across the root upon exposure to unfavourable conditions on the opposite side. Our approach sheds light on lateral coordination of morphological adaptation and facilitates studies on root physiology, signalling and development in heterogeneous environments at the organ level.

plant biology↗