Biology subjects

Wabnik, K.

Publications and source records attributed to Wabnik, K..

11 recordsLinked to original sources

bioRxiv2026

Cell wall charge gates iron availability in plant roots

Plants acquire essential mineral nutrients from the soil, yet these elements must first traverse the extracellular matrix of the root before reaching the cell surface. How the physical properties of this extracellular compartment influence nutrient distribution and availability remains poorly understood. In plants, this extracellular matrix is formed by the cell wall, which carries a dynamically regulated negative charge that can change during development and in response to environmental cues. Here we demonstrate that cell wall charge functions as a tunable electrostatic gate that determines how iron is partitioned between retention and bioavailability. This decoupling between iron abundance and availability reveals a fundamental tradeoff imposed by extracellular electrostatics. A mechanistic diffusion-binding model shows that increasing wall charge inherently enhances iron sequestration while limiting its mobility at the cell surface. Genetic perturbation of pectin de-methylesterification validates this principle in vivo. Moreover, iron limitation itself triggers active remodeling of cell wall charge, dynamically shifting the balance toward increased iron accessibility. Together, these findings identify the plant cell wall as an active regulator of nutrient homeostasis rather than a passive barrier. By dynamically modulating extracellular electrostatics, roots control iron partitioning and bioavailability, uncovering a new physical layer of regulation in plant mineral nutrition. One-Sentence SummaryThe plant cell wall operates as a tunable electrostatic gate that buffers and releases iron through spatially and environmentally regulated charge dynamics.

plant biology↗

bioRxiv2026

Differential photoperiodic control of morning and evening expressed transcripts in tomato

Photoperiod, the daily duration of light, is a key environmental cue that varies with season and latitude. Photoperiod signals profoundly influence plant growth and development, and play a central role in crop adaptation across latitudes. Deciphering how plants perceive these seasonal light cues at the molecular level is essential for understanding crop evolution and shaping their geographical distribution. In this study, we investigated how photoperiod influences gene expression dynamics in tomato (Solanum lycopersicum) by performing an RNA-seq time-course across three photoperiod regimes, sampling at two-hour intervals. We use isogenic lines segregating for wild alleles of genes involved in circadian rhythm domestication in tomato to describe their contributions to the circadian clock and flowering time pathways. The high temporal resolution of our experiment allowed precise characterization of transcriptional dynamics and their responses to photoperiod, including shifts in phase, amplitude, and waveform. We found that most transcripts time their expression to dawn or approximately 12 hours later, resulting in a systematic misalignment between evening transcripts and the actual timing of dusk. Morning- and evening-phased transcripts differ markedly in expression levels and waveform responses to changes in photoperiod. Together, these patterns suggest that morning transcripts sense photoperiod transcriptionally, and serve as zeitgeber references for evening transcripts, that could measure photoperiod length by coincidence with external cues. Together, our results provide new insight into the molecular basis of photoperiodic adaptation in plants.

plant biology↗

bioRxiv2026

Mechanical coordination of counter-gradient growth maintains organ curvature in apical hooks

How growing tissues convert mechanical tension into signals that stabilize form remains a central question in morphogenesis. Curved organ shapes in plants arise from differential growth, yet how such curvature is actively maintained while organs continuously grow remains poorly understood. In etiolated seedlings, the apical hook provides a tractable model to dissect this process, as its curvature is stably maintained over extended periods despite ongoing cell expansion. Using quantitative imaging and computational modeling, we show that antagonistic growth gradients at apical and basal regions are both necessary and sufficient to maintain hook curvature, with cuticle integrity being critical for establishing these counter-gradients. Mechanical cues linked to cuticle structure, coupled with apoplastic reactive oxygen species (ROS), coordinate cellular growth anisotropy, and disruptions in cuticle biosynthesis trigger defective hook development. These findings reveal that the apical hook curve maintenance is not a simple switch between growth promotion and repression, but a highly dynamic, tightly regulated process where mechanical and biochemical signals coordinate organ-scale morphogenesis, fundamentally reshaping how we understand developmental growth.

plant biology↗

bioRxiv2023

Competing differentiation gradients coordinate fruit morphogenesis

Morphogenesis requires the coordination of cellular behaviors along developmental axes1. In plants, gradients of growth and differentiation are typically established along a single longitudinal primordium axis to control organ shaping2. Here we combine quantitative live-imaging at cellular resolution with genetics, chemical treatments, and modeling to understand the formation of Arabidopsis thaliana female reproductive organ (gynoecium). We show that, contrary to other aerial organs, gynoecium shape is determined by two competing differentiation gradients positioned along two orthogonal axes. An early mediolateral gradient, dependent on meristematic activity in the medial domain, controls the valve morphogenesis while simultaneously restricting an auxin-dependent, longitudinal gradient to the style. This gradient competition serves to finetune the common developmental program governing organ morphogenesis to ensure the specialized function of the gynoecium3,4.

plant biology↗

bioRxiv2022

A quorum of mechano-sensing fungal consortia

Bacteria use Quorum sensing (QS) to coordinate gene expression in dense cell populations. Here, we show that eukaryote S. Cerevisiae uses an alternative strategy, the quorum mechano-sensing (QMS), to resolve growth conflicts in the fungal consortia. QMS connects the biomechanical signal perception through adhesin FLO11 and transmembrane histidine kinase SLN1, triggering an intracellular signaling cascade for the cell density-dependent regulation of gene expression. Both cis and trans interactions of FLO11 are required for the inhibition of SLN1 and involve the extracellular fibronectin type III-like domain of FLO11. Genetic deletion of FLO11 removes inhibition of SLN1, associated with the spontaneous activation of gene expression whereas overproduction of FLO11 strengthens the inhibitory effect of FLO11 on SLN1. Therefore, adjusting the amount of FLO11 directly scales with the level of SLN1 inhibition, forecasting the outcome of growth competition at the macroscopic scale. Furthermore, the integration of an orthogonal synthetic circuit downstream of SLN1 allows for QMS-controlled regulation of gene expression in cell populations. Our study reveals a molecular pathway connecting FLO11 adhesion to SLN1-dependent intracellular regulation of gene expression in fungi. FLO11 and SLN1 coordinate kin recognition and growth conflict resolution through gene expression in dense fungal populations. This study challenges the classical view of chemically-driven QS and provides new strategies for controlling population growth through quorum mechano-sensing.

microbiology↗

bioRxiv2022

Stem cell regulators control a G1 duration gradient in the plant root meristem

In meristems, where new plant organs initiate, key stem cell regulators have been identified, but their link to cell cycle progression remains unclear. Here, we show that the root meristem has a positional gradient of G1 duration that ranges from [~]2 h near the meristem boundary to more than 20 h in stem cells and early derivatives. Mutants in the PLETHORA (PLT) genes shortened G1 length and flattened its gradient. Computer modeling of an incoherent feed-forward loop (IFFL) predicted the inference of a negative regulatory pathway. We propose that PLT genes play opposing roles, maintaining meristem and stem cell activity and inhibiting G1 progression through the CDK inhibitor KRP5, a PLT target, and RBR1. This establishes a previously undescribed proximal-distal feature of the root meristem in which a G1 duration gradient is shaped by stem cell and meristem maintenance regulators.

plant biology↗

bioRxiv2022

Macroscopic chemical to electrical signal converter in microbial communities

Excitable cells can convert electrical signals into chemical outputs to facilitate the active transport of information across larger distances. This electrical-to-chemical conversion requires a tightly regulated expression of ion channels. Alterations of ion channel expression provide landmarks of numerous pathological diseases, such as cardiac arrhythmia, epilepsy, or cancer. Although the activity of ion channels can be locally regulated by external light or chemical stimulus, it remains challenging to coordinate the expression of ion channels on extended spatial-temporal scales in a non-invasive manner. Here, we have engineered yeast S. cerevisiae to read and convert local chemical concentrations into a dynamic electrical field distributed across cell populations. The core mechanism encodes a chemically-excitable dual-feedback gene circuit that precisely tunes the expression domain of potassium channels, globally coordinating cyclic firing of the plasma membrane potential (PMP). We demonstrate that this mechanism leverages an engineered constitutively open bacterial potassium channel KcsA to directly couple chemical stimuli with ion flux through gene expression and it can interface with the host ion channels through the pulsatile production of toxins. Our study provides a robust synthetic transcriptional toolbox underlying the conversion of local chemical environments into spatiotemporally organized electrical impulses for various cellular engineering, synthetic biology, and potential therapeutic applications.

synthetic biology↗

bioRxiv2021

Design principles of plant root morphogenesis

Plants grow roots to adjust their bodies to dynamic changes in the surrounding environment. How do plant roots emerge from the stem cell reservoir during embryogenesis is however poorly understood. Here, we present a bottom-up strategy to address this challenge by combining empirical observations with advanced computer modeling techniques. We demonstrate that the anisotropy of root growth results from differential growth rates of adjacent tissues, whereas the root meristem development incorporates a multi-level feedback loop between complex transport network of phytohormone auxin, auxin-dependent cell growth and cytoskeleton rearrangements. In silico model predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our findings reveal a minimal set of design principles connecting tissue mechanics, cell anisotropy, and directional transport that are sufficient for self-organization of the root meristem shape. A mobile auxin signal transported through immobile cells orchestrates polarity and growth mechanics to instruct the morphogenesis of an independent organ.

plant biology↗

bioRxiv2020

Modulation of root growth by nutrient-defined fine-tuning of polar auxin transport

Nitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, live in vivo high- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth, i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.

plant biology↗

bioRxiv2020

Synthetic biosensor circuits generate a frequency-encoded response to phytohormones under a dynamic environment

How do dynamic hormone inputs translate into speed, and precision of response is one of the most challenging questions of science. To approach this question, we constructed minimal synthetic gene circuits capable of responding to plant hormones auxin and salicylic acid (SA). These circuits integrate bacterial multi antibiotic resistance (Mar) repressors that directly detect phytohormones through a ligand-induced conformational switch. The combination of individual circuits in synthetic auxin-SA crosstalk was sufficient to coordinate responses across the cell population with tunable precision and speed in long-term microfluidics experiments. This antagonistic auxin-SA crosstalk retains temporal memory upon extended exposure to hormones and synchronizes the behavior of individual cells with the environmental clock. Our study shows how dynamic hormone inputs can be translated in robust and precise responses with a minimal assembly of bacterial transcriptional repressors, suggesting an alternative regulatory strategy to known plant hormone signaling systems.

synthetic biology↗

bioRxiv2019

Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots

Directional organ growth allows the plant root system to strategically cover its surroundings. Intercellular auxin transport is aligned with the gravity vector in the primary root tips, facilitating downward organ bending at the lower root flank. Here we show that cytokinin signaling functions as a lateral root specific anti-gravitropic component, promoting the radial distribution of the root system. We performed a genome-wide association study and revealed that signal peptide processing of Cytokinin Oxidase 2 (CKX2) affects its enzymatic activity and, thereby, determines the degradation of cytokinins in natural Arabidopsis thaliana accessions. Cytokinin signaling interferes with growth at the upper lateral root flank and thereby prevents downward bending. Our interdisciplinary approach revealed that two phytohormonal cues at opposite organ flanks counterbalance each others negative impact on growth, suppressing organ growth towards gravity and allow for radial expansion of the root system.

plant biology↗