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Research

Research

We combine live imaging, biochemistry,spatial omicsand developmental biology to uncover howlight perception and signaling are spatially regulated.Our lab has two main foci:

The formation and function of phytochrome subnuclear bodies (Photobodies)
HY5 shoot to root transport; Far-Red light effect on root development.

We combine live imaging, biochemistry,spatial omicsand developmental biology to uncover howlight perception and signaling are spatially regulated.Our lab has two main foci:

The formation and function of phytochrome subnuclear bodies (Photobodies)
HY5 shoot to root transport; Far-Red light effect on root development.

Research

We are studying how light perception and light signalling is spatially integrated within the nucleus, cells and tissues of plants.​

Background & Approach:
Cell Biology of Light Signaling

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Plant photoreceptors can be found in almost all cells of the plant body, and within these cells, they cluster into subnuclear phase-separated compartments, which are large protein bodies that help concentrate, aggregate, and regulate the factors that determine how the plant reacts to light, temperature, and other environmental factors. Furthermore, we study how the root can react to shoot-perceived light through the action of shoot-to-root mobile transcription factors.

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In our studies we use various imaging techniques such as confocal (live) imaging, super-resolution light microscopy, transmission electron microscopy and cryo-electron tomography. We complement this with molecular biology, biochemistry and protein structure modelling techniques to study protein-protein interactions. To study the effects of light signalling, besides standard molecular genetics techniques, we use single nucleus transcriptomics and mathematical modelling to unravel tissue and cell-specific aspects. This interdisciplinary approach helps us to understand how light receptor complexes function within tissues and at the structural level.

Phytochrome photobody formation and function

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Phytochromes are the main red light sensors in plants, and they form small (~500 nm) subnuclear bodies, which also contain supporting cofactors and downstream transcription factors. These subnuclear structures are called photobodies, and they play an important role in regulating light responses. Importantly, phytochrome B (phyB) is required not only for light sensing but also for temperature sensing, suggesting that photobodies play an important role in plant responses to ambient temperature.

Despite their importance, it remains unclear how the formation of photobodies aids phytochrome signaling, how output specificity is achieved in response to divergent stimuli, and how this information influences plant developmental decisions. The formation of nuclear bodies is a general process in the eukaryotic nucleus, and lessons learned from photobodies may help us understand nuclear organization in general.

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To tackle these fundamental questions, we investigate the formation and responses of photobodies to light and temperature using an integrated approach of high-resolution live imaging and biochemistry. Using LEDs, we create a dynamic light environment at the confocal microscope to produce time-lapse images of nuclei, such as the movie depicted here (use the movie from the main page). Furthermore, we are employing proximity labeling to discover the composition of photobodies and chemical imaging screens to identify new photobody-manipulating drugs.

This project is funded by the DFG Emmy Noether Programme.

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In addition, we are investigating the commonalities between photobodies by looking at a photobody-localizing protein and crucial light response factor, CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1). COP1 was one of the first plant proteins to be observed in nuclear phase-separated bodies and has been heavily studied over the years, with many functions uncovered in regulating the plant light response. However, there has been comparatively little study on how COP1 localizes to photobodies and how that relates to phytochromes. By using similar techniques as described for phyB photobodies, we aim to uncover the role of COP1 in forming and maintaining photobodies. This project is funded by a DAAD–India fellowship.

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HY5
shoot-to-root transport

Plants can see competitors through the reflection of far-red light from neighbouring plant leaves, which helps them to avoid future competition for light, their sole energy source. A decrease in the red:far-red light ratio is perceived by phytochrome photoreceptors and leads to elongation responses above ground. However, low red:far-red detection by the shoot also prompts plants to reduce their root growth, possibly to conserve resources. An important regulator in this response is the transcription factor ELONGATED HYPOCOTYL 5 (HY5), which can be transported from the shoot to the root. There, it has the ability to suppress auxin signaling and lateral root outgrowth. However, the mechanics of HY5 transport are not yet well understood, and it is not clear whether the transport of HY5 is the direct link between shoot-detected far-red light and a decrease in lateral root outgrowth.​

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​Therefore, we study the mechanics and speed of HY5 transport using confocal microscopy and HY5-inducible lines. We have constructed shoot-specific inducible lines to perform live imaging of this transport with a vertical confocal microscope. With this setup, we are able to follow the transport and unloading of HY5 from the phloem into the phloem pole pericycle, where it enters the nucleus. The question we are tackling now is how the shoot-borne HY5 is different from the root-borne HY5. Besides the aforementioned microscopy, we are also employing micrografting, detailed phenotyping, proximity labelling, and single-nucleus sequencing. The project is funded by a DFG Walter Benjamin grant and a DAAD–Pakistan fellowship.

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Recently, we have published, together with the lab of Ronald Pierik, our findings on the role of gibberellins in shoot–root communication in far-red-induced shade avoidance. Gibberellic acid (GA) is a crucial plant hormone in regulating growth, and we have identified that it can play a role in mediating shoot–root signaling via the transport of GA through the phloem. GA itself has an effect on the protein amounts of HY5, and GA also affects auxin signalling through its DELLA repressor proteins. This work is summarized in the figure above. In the future, we will continue to place our findings on HY5 shoot–root transport in a wider context of hormonal and growth regulation, also via mathematical modelling of growth processes.

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Scientific Results

  1. van Gelderen K, van der Velde K, Kang C, Hollander J, Koppenol A, Petropoulos O, Prasetyaningrum P, Akyüz T, and Pierik R. (2025) Gibberellin transport affects lateral root growth through HY5 in response to far-red light. Plant Cell. 2025:37(9):koaf200. https://doi.org/10.1093/plcell/koaf200 (OA)

  2. van Gelderen K, van der Velde K, Kang C-K, Hollander J, Petropoulos O, Akyuz T, Pierik R. (2023). Gibberellin transport affects (lateral) root growth through HY5 during Far-Red light enrichment. BioRxiv doi:10.1101/2023.04.21.537844 (OA)

  3. González J and van Gelderen K (2021) Bundling up the Role of the Actin Cytoskeleton in Primary Root Growth. Front. Plant Sci. (2021)  
    doi: 10.3389/fpls.2021.777119 (OA)      

  4. Glanc M & , Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarová L, Hauschild R, Johnson A, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R and Friml J (2021) 31: 449-451. doi: 10.1016/j.cub.2021.02.028 (OA) *Authors contributed equally

  5. van Gelderen K, Kang C, Li P and Pierik R (2021) Regulation of lateral loot development by shoot-sensed far-red light via HY5 is nitrate-dependent and involves the NRT2.1 nitrate transporter. Front. Plant Sci. doi: 10.1101/2021.01.31.428985 (OA)  

  6. van Gelderen K (2021) GAPs in ROP microdomains help establish cell polarity, Plant Physiology 187, 2348–2349, https://doi.org/10.1093/plphys/kiab460 (OA) News and views.

  7. van Gelderen K (2021) Can I have some light and sugar with my nitrate? Plant Physiology 186, 196–197, https://doi.org/10.1093/plphys/kiab068 (OA) News and views.

  8. Buti S, Pantazopoulou CK, , Hoogers VAC, Reinen E and Pierik R (2020) A gas-and-brake mechanism of bHLH proteins modulates shade avoidance in Arabidopsis thaliana. Plant Physiology 184: 2137–2153. doi: 10.1104/pp.20.00677 (OA)

  9. van Gelderen K (2020) A High-Five for High Light Protection, Plant Physiology 184, 570–571, https://doi.org/10.1104/pp.20.01212 (OA) News and views.

  10. van Gelderen K (2020) True Blue: How Cry1 Inhibits Phototropism in Green Seedlings, Plant Physiology 184, 4-5, https://doi.org/10.1104/pp.20.01013 (OA) News and views.

  11. van Gelderen K (2020) The Rhythm of the Light: How Light and the Clock Drive Cycling of Transcript Levels in Barley, Plant Physiology 183, 441-442, https://doi.org/10.1104/pp.20.00360 (OA) News and views.

  12. van Gelderen K (2020) Photosynthesis in the Womb: Does Embryonic Photosynthesis Give Seedlings a Head Start? Plant Physiology 182, 1817-1818 https://doi.org/10.1104/pp.20.00264 (OA) News and views.

  13. van Gelderen, K., Pierik, R. (2020) Warm days, relaxed RNA. Nature Plants 6, 438–439 https://doi.org/10.1038/s41477-020-0643-1 News and views.

  14. Hayes S, Pantazopoulou CK, , Reinen E, Tween AL, Sharma A, de Vries M, Prat S, Schuurink RC, Testerink C, and Pierik R (2019) . 29: 360-362. doi: 10.1016/j.cub.2019.03.042

  15. van Gelderen K, Kang C, Paalman R, Keuskamp D, Hayes S, and Pierik R (2018) Far-Red Light Detection in the Shoot Regulates Lateral Root Development through the HY5 Transcription Factor. The Plant Cell 30: 101–116. doi: 10.1105/tpc.17.00771 (OA)  

  16. van Gelderen K, Kang C, and Pierik R (2018) Light Signaling, Root Development, and Plasticity. Plant Physiology 176: 1049–1060. doi: 10.1104/pp.17.01079 (OA)

  17. Küpers JJ, , and Pierik R (2018) Location Matters: Canopy Light Responses over Spatial Scales. Trends in Plant Science 23: 865–873.           
    doi: 10.1016/j.tplants.2018.06.011 (OA)

  18. van Gelderen K, van Rongen M, Liu A, Otten A, and Offringa R (2016) An INDEHISCENT-Controlled Auxin Response Specifies the Separation Layer in Early Arabidopsis Fruit. Molecular Plant 9: 857–869. doi: 10.1016/j.molp.2016.03.005

  19. Postma W.J., Slootweg E.J., Rehman S., Finkers-Tomczak A., Tytgat T.O.G., , Lozano-Torres J.L., Roosien J., Pomp R., van Schaik C., Bakker J., Goverse A., Smant G. (2012). 160: 944–54. DOI: 10.1104/pp.112.200188

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