Biology subjects

van Gelderen, K.

Publications and source records attributed to van Gelderen, K..

5 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↗

bioRxiv2026

phyB photobodies display molecular memory, regulating light signaling transcriptional states through phase separation.

Phytochrome B is a crucial red and far-red light sensor, which controls plant development and environmental responses to light and temperature. In the nucleus, phyB forms phase separated condensates, also called photobodies, consisting of various transcriptional regulators and transcription factors. phyB photobodies can form or disperse depending on the amount of light, the light quality, or ambient temperature. However, the biological relevance for forming photobodies is still unclear. In recent years the study of condensates has given rise to the idea that condensates can act as molecular memory, either due to long equilibration timescales arising from strong interactions can kinetically trap a mixture in a phase-separated state beyond the equilibrium coexistence line, or from phase-separation dependent modification processes or transcriptional regulation. Here, we hypothesize that the formation of phyB photobodies and the associated sequestration of signaling molecules allows for the formation of cell-type specific memory about light conditions. To address this hypothesis, we first developed a live imaging setup of phyB photobodies which shows that they do not follow classic liquid-liquid phase separation dynamics, but instead have a restriction on their size, intensity and minimum number. Fluorescence recovery after photobleaching (FRAP) then showed that photobodies between cell types have different levels of mobilities and diffusivities, suggesting that they are more stable in darkness or high red light, versus low red light. These differences in phyB photobody stability between cell types were also confirmed through whole-mount confocal imaging and single-nucleus transcriptomics in the same light-perturbation series. Through sci-Seq single nucleus spatial transcriptomics of the cotyledon in this light perturbation series, we identify a photobody-associated transcriptional cluster of nuclei that regulates photosynthesis, circadian rhythm, and RNA processing; the phyB photobody likely promotes its own stability by regulating TZP and PCH1 expression. The correlation between photobodies and transcriptional regulation shows how phyB condensates can provide cell-type specific light responses and exhibit signaling memory in changing environmental conditions.

cell biology↗

bioRxiv2021

Regulation of lateral root development by shoot-sensed far-red light via HY5 is nitrate-dependent and involves the NRT2.1 nitrate transporter.

Plants are very effective in responding to environmental changes during competition for light and nutrients. Low Red:Far-Red (low R:FR)-mediated neighbor detection allows plants to compete successfully with other plants for available light. This above-ground signal can also reduce lateral root growth by inhibiting lateral root emergence, a process that might help the plant invest resources in shoot growth. Nitrate is an essential nutrient for plant growth and Arabidopsis thaliana responds to low nitrate conditions by enhancing nutrient uptake and reducing lateral and main root growth. There are indications that low R:FR signaling and low nitrate signaling can affect each other. It is unknown which response is prioritized when low R:FR light- and low nitrate signaling co-occur. We investigated the effect of low nitrate conditions on the low R:FR response of the A. thaliana root system in agar plate media, combined with the application of supplemental Far-Red (FR) light to the shoot. We observed that under low nitrate conditions main and lateral root growth was reduced, but more importantly, that the response of the root system to low R:FR was suppressed. Consistently, a loss-of-function mutant of a nitrate transporter gene NRT2.1 lacked low R:FR-induced lateral root reduction and its root growth was hypersensitive to low nitrate. ELONGATED HYPOCOTYL5 (HY5) plays an important role in the root response to low R:FR and we found that it was less sensitive to low nitrate conditions with regards to lateral root growth. In addition, we found that low R:FR increases NRT2.1 expression and that low nitrate enhances HY5 expression. HY5 also affects NRT2.1 expression, however, it depended on the presence of ammonium in which direction this effect was. Replacing part of the nitrogen source with ammonium also removed the effect of low R:FR on the root system, showing that changes in nitrogen sources can be crucial for root plasticity. Together our results show that nitrate signaling can repress low R:FR responses and that this involves signaling via HY5 and NRT2.1.

plant biology↗

bioRxiv2020

A gas-and-brake mechanism of bHLH proteins modulates shade avoidance in Arabidopsis thaliana

Plants detect proximity of competitors through reduction in the ratio between red and far red light triggering the shade avoidance syndrome, which includes accelerated shoot elongation and early flowering. Shade avoidance is regulated through PHYTOCHROME INTERACTING FACTORs (PIFs), a group of bHLH transcription factors. Another (b)HLH protein, KIDARI (KDR), which is non-DNA-binding, was identified in de-etiolation studies and proposed to interact with LONG HYPOCOTYL IN FAR-RED 1 (HFR1), a (b)HLH protein that inhibits shade avoidance. Here we establish novel roles of KDR in regulating shade avoidance and investigate how KDR regulates the shade avoidance network. We show that KDR is a positive regulator of shade avoidance and interacts with several negative growth regulators. We identify novel interactors using a combination of yeast two-hybrid screening and dedicated confirmations with bimolecular fluorescence complementation. We demonstrate that KDR is translocated primarily to the nucleus when coexpressed with these newly discovered interactors. A genetic approach confirmed that several of these novel interactions are indeed functional to shade avoidance in Arabidopsis thaliana, whereas we propose that KDR does not interact with HFR1 to regulate shade avoidance. Based on this, we propose that shade avoidance is regulated by a three-layered gas-and-brake mechanism of bHLH protein interactions, adding an additional layer of complexity to what was previously known. One-sentence summaryKIDARI is a positive regulator of shade avoidance and part of a three-layer network of bHLH transcription factor interactions.

plant biology↗

bioRxiv2018

Soil salinity inhibits plant shade avoidance

Global food production is set to keep increasing despite a predicted decrease in total arable land [1]. To achieve higher production, denser planting will be required on increasingly degraded soils. When grown in dense stands, crops elongate and raise their leaves in an effort to reach sunlight, a process termed shade-avoidance [2]. Shade is perceived by a reduction in the ratio of red (R) to (FR) light and results in the stabilisation of a class of transcription factors known as PHYTOCHROME INTERACTING FACTORs (PIFs) [3,4]. PIFs activate the expression of auxin biosynthesis genes [4,5] and enhance auxin sensitivity [6], which promotes cell wall loosening and drives elongation growth. Despite our molecular understanding of shade-induced growth, little is known about how this developmental programme is integrated with other environmental factors.\n\nHere we demonstrate that low levels of NaCl in soil strongly impair the ability of plants to respond to shade. This block is dependent upon abscisic acid (ABA) signalling and the canonical ABA signalling pathway. Low R:FR light enhances the expression of a positive regulator of the brassinosteroid (BR) signalling pathway, BRASSINOSTEROID SIGNALLING KINASE 5 (BSK5). We found that ABA inhibits BSK5 up-regulation and interferes with GSK3-like kinase inactivation by the BR pathway, thus leading to a suppression of PIF function. By demonstrating a link between the ABA and BR-signalling pathways this study provides an important step forward in our understanding of how environmental cues are integrated into plant development.

plant biology↗