Biology subjects

Retzer, K.

Publications and source records attributed to Retzer, K..

8 recordsLinked to original sources

bioRxiv2026

Shoot to root transport of the HY5 transcription factor drives root developmental plasticity under neighbour shade.

Plants perceive competitors through the reflection of Far-Red light from neighbouring leaves. A decrease in the Red: Far-red light ratio (R:FR) is perceived by phytochrome photoreceptors and triggers elongation responses aboveground, allowing plants to anticipate future competition for light; their primary energy source. However, low R:FR perception by the shoot also prompts an alteration of root development, possibly to conserve resources. An important regulator of this response is the bZIP transcription factor ELONGATED HYPOCOTYL 5 (HY5), which can be transported from the shoot to the root, where it suppresses auxin signaling and lateral root outgrowth. However, it remains unknown whether HY5 transport is the direct link between shoot-perceived low R:FR and a decrease in lateral root outgrowth. We therefore sought to uncover the mechanics and speed of HY5 transport. To this end, we constructed shoot-specific inducible lines to perform live-imaging of HY5 transport using a vertical confocal microscope. This allowed us to follow the transport and unloading of HY5 from the phloem into the protophloem pericycle, where it becomes nuclearly localized, in real time over a 24-hour period. To mimic plant competition, we applied supplemental FR light and observed that this increased the HY5 protein levels in the shoot and subsequent HY5 protein transport from shoot-to-root. Finally, we were able to show that shoot-expressed HY5 is necessary and sufficient to induce the root response to shoot perceived Far-Red light. This work showcases in detail how a small general transcription factor functions as a long-distance signal between shoot and root and integrates environmental signalling over long distances in the plant.

plant biology↗

bioRxiv2025

SnRK1.1 Coordinates Organ-Specific Growth-Defense Programs via Transcriptomic Rewiring in Arabidopsis thaliana

SnRK1 (Sucrose non-fermenting-1-Related Kinase 1) is a master regulator of cellular energy homeostasis in plants, coordinating developmental and metabolic responses under environmental and internal stress conditions. Here, we demonstrate that its catalytic subunit, KIN10, orchestrates organ-specific growth-defense programs in Arabidopsis thaliana through transcriptomic rewiring. Using RNA-seq profiling, we reveal that kin10 knockout mutants exhibit extensive transcriptional reprogramming in roots, particularly in pathways linked to signal perception, cell wall remodeling, and intracellular trafficking, which correlates with impaired root growth and reduced root hair elongation upon Pseudomonas syringae infection. In contrast, KIN10 overexpression (KIN10-OE) lines display constitutive defense activation in shoots, including elevated expression of genes associated with reactive oxygen species (ROS) production and salicylic acid (SA) signaling, leading to enhanced ROS accumulation and growth trade-offs. kin10 roots show muted responses to biotic stimuli, while KIN10-OE shoots prioritize defense over growth. These findings position KIN10 as a critical integrator of energy status and immune signaling, enabling fine-tuned, tissue-specific responses essential for optimizing plant adaptation to dynamic environmental challenges.

plant biology↗

bioRxiv2025

Analysing the Role of KIN10 in Directional Root Growth Regulation in Arabidopsis thaliana

Root growth directionality is critical for plant survival, optimizing anchorage and resource acquisition. While the role of hormonal signaling in root gravitropism is well established, the contribution of metabolic status remains less understood. Here, we investigate the function of the catalytic SnRK1 subunit KIN10 in integrating carbon availability with root growth regulation in Arabidopsis thaliana. A combination of growth phenotyping, transcriptomics, and hormonomic profiling suggest that KIN10 loss disrupts energy-linked developmental processes. Compared to wild-type Col-0, kin10 displayed reduced sensitivity to glucose-induced root growth inhibition. Transcriptomic analysis of kin10 roots revealed widespread reprogramming of metabolic and hormonal pathways, with significant changes in secondary metabolism, cell wall remodeling, and hormone-related gene expression. Hormone profiling further indicated that KIN10 modulates auxin and jasmonate pathways in a carbon source- and organ-dependent manner, especially under sucrose supplementation. Our results demonstrate that KIN10 plays a central role in integrating energy status with developmental and environmental signaling.

plant biology↗

bioRxiv2025

Nanodomain distribution and function of PIN-FORMED auxin efflux carriers in the plasma membrane of tobacco cells are defined by their interactions with the cell wall

Plant development is under the morphogenic control of auxin. In addition to biosynthesis and metabolism, auxin concentration gradients are maintained by directional intercellular transport via PIN-FORMED (PIN) auxin efflux carriers. Although the structure-function properties of PINs have been described, it is still unclear whether individual members of PIN family could localize differently within the plasma membrane (PM) and whether their nanodomain distribution defines their function. To address this, we used cultured tobacco cells (Nicotiana tabacum L., cv. BY-2) and revealed by RNA-seq and RT-qPCR the cell stage-specific presence of transcripts of tobacco PIN homologs. We used high-resolution light microscopy and two independent immunoelectron microscopy techniques in cell lines expressing functional GFP-tagged inducible versions of NtPIN11T, NtPIN2T and NtPIN3bT. We show that NtPINs are distributed within specific PM nanodomains and that removal of the cell wall alters their appearance. By a series of in vivo microscopic observations, we provide evidence that NtPIN11T is the most homogenously distributed and the least mobile NtPIN. Pharmacological treatments suggested that the immobilization of NtPIN11T depends on the actin and microtubular cytoskeleton and the cell wall composition. Using comparative co-immunoprecipitation (co-IP) analysis of isolated membrane fractions for all three NtPINs we finally identified several novel interaction partners indicating a preferential association of NtPIN11T with cell wall GPI-anchored arabinogalactan proteins. In conclusion, our results suggest a model in which specific immobilization of PINs through interactions with the cell wall affects their function.

plant biology↗

bioRxiv2024

Dynamic Dark Root Chamber: Advancing non-invasive phenotyping of roots kept in darkness using infrared imaging

Root phenotyping is a challenging task that would require monitoring root growth in soil under dark conditions to mimic natural conditions, while allowing the shoot to grow in light. Most existing methods involve exposing the roots to light, which substantially alters their growth and function. In this paper, we present an improved imaging system that can overcome this limitation of experiments performed in laboratories. The Dynamic Dark Root imaging Chamber (DDrC) enables continuous monitoring and image acquisition to track the dynamic development of root architecture under controlled growth conditions. Our imaging system is based on a Raspberry Pi camera module and infrared LEDs, which do not induce any stress responses in the roots. The DDrC setup is simple, affordable, and suitable for dynamic phenotyping experiments. We provide a detailed tutorial for the assembly and adjustment of the imaging chamber. We conclude that our system is a valuable tool for studying the genetic and environmental factors that affect the root system architecture and development, and for identifying the root traits that are related to plant adaptation and performance.

plant biology↗

bioRxiv2022

RaPiD-chamber: Easy to self-assemble live-imaging chamber with adjustable LEDs allows to track small differences in dynamic plant movement adaptation on tissue level

Plants rely on fine-tuning organ movement to ensure their survival and productivity. Even subtle loss of directional growth orchestration can result in a huge impact when the plant is impaired to adapt to an ever-changing environment, where it is exposed to manifold exogenous stimuli simultaneously. We present a newly designed chamber to obtain live images to track organ growth and movement differences, called RaspberyPi Dark Chambers (RaPiD-chamber). The RaPiD-chamber is easy to self-assemble and cost-efficient and allows to monitor the continuous growth of etiolated seedlings, as well as their response to light of different wavelengths and from chosen positions. We tested the advice by comparing hypocotyl elongation rate and response to unilateral white and blue light exposure of Arabidopsis thaliana Col0. Additionally, we compared the elongation rate of etiolated hypocotyls between Col0 and kin10, a mutant lacking the catalytic subunit of the cellular signaling hub SUCROSE NON-FERMENTING RELATED KINASE 1 (SnRK1). kin10 is known for its diminished ability to control hypocotyl elongation. As a case study, we compared the growth dynamics of etiolated Col0 versus kin10. Without further energy source supplementation to the growth medium, the mutant cannot keep up with hypocotyl elongation. Additionally, continuous observation of the dark-grown seedlings allowed us to determine a shift in the dynamics of apical hook angle formation for the mutant.

plant biology↗

bioRxiv2021

Continuous tracking of gravistimulated roots in a chambered coverslip by confocal microscopy allows first glimpse on mechanoadaptation of cell files during curvature initiation

Mechanical responses of individual cells to plant internal and external stimuli modulate organ movement and ensure plant survival as sessile organism in a constantly changing environment. The root is a complex, three-dimensional object, which continuously modifies its growth path. Autonomous and paratonic root movements are both orchestrated by different signaling pathways, whereby auxin modulated directional growth adaptations, including gravitropic response, were already subject of manifold studies. But we still know very little about how cells adapt upon gravitropic stimulus to initiate curvature establishment, which is required to align root tip growth again along the gravitropic vector. This manuscript shows first insights into cell file movements upon gravitropic stimulus of Arabidopsis thaliana roots that initiate curvature establishment. The roots were grown shaded from light and without exogenous sucrose supplementation, both growth conditions that are known to negatively interfere with directed root growth, which allowed a more uniform tracking of root bending by using a confocal microscope with vertical stage.

plant biology↗

bioRxiv2020

A role of DAO1 in oxidation of IAA amino acid conjugates revealed through metabolite, high throughput transcript and protein level analysis.

Auxin metabolism is, together with auxin transport, a key determinant of auxin signalling output in plant cells, yet details on the underlying mechanisms and factors involved are still largely unknown. Processes involved in the auxin metabolism are subject to regulation based on numerous signals, including auxin concentration itself. Altered auxin availability and the subsequent changes of auxin metabolite profiles can therefore elucidate the function and regulatory role of individual elements in the auxin metabolic machinery. After analysing auxin metabolism in auxin dependent tobacco BY-2 cell line grown in presence or absence of synthetic auxin 2,4-D we found that both conditions were similarly characterized by very low levels of endogenous indole-3-acetic acid (IAA) and its metabolites. However, metabolic profiling after exogenous application of IAA uncovered that the concentration of N-(2-oxindole-3-acetyl)-L-aspartic acid (oxIAA-Asp), the most abundantly formed auxin metabolite in the control culture, dramatically decreased in auxin-starved conditions. To describe the molecular mechanism behind this regulation, we analysed transcriptome and proteome changes caused by auxin starvation. While no changes in the expression of auxin biosynthetic machinery were observed, many genes related to auxin conjugation and degradation showed differential expression. Selected putative auxin glycosylating enzymes as well as members of the Gretchen Hagen 3 gene family involved in auxin amino acid conjugation showed both up- and down-regulation. Contrarily to that, all tobacco homologs of Arabidopsis thaliana DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), known to be responsible for the formation of oxIAA from IAA, showed significant downregulation at both transcript and protein levels. To validate the role of DAO1 in auxin metabolism, we performed auxin metabolite profiling in BY-2 mutants carrying either siRNA-silenced or CRISPR-Cas9-mutated NtDAO1, as well as in dao1-1 Arabidopsis thaliana plants. Both mutants showed not only expectedly lower levels of oxIAA, but also significantly lower abundance of oxidated amino acid conjugates of IAA (oxIAA-Asp). Our results thus represent the first direct evidence on DAO1 activity on IAA amino acid conjugates. Statement of significanceHere we present an analysis of auxin metabolism on metabolite, transcript and protein levels in tobacco BY-2 cell line, collectively identifying oxidation of IAA amino acid conjugates as a new role of DIOXYGENASE FOR AUXIN OXIDATION 1 within an auxin-level-responsive metabolic system.

plant biology↗