Group of MECHANOMICS of directional root growth

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Exogenous stimuli induce directional root growth deviation and regulated shootward auxin distribution is required to oppose the stimulus

As sessile organisms, plants rely on fine-tuning organ movement to ensure their survival and productivity. Even a subtle loss of directional growth orchestration can have a big impact on plant growth. Roots are three-dimensional objects that grow embedded by soil, and to adjust root movement they regulate direction of root growth by altering cell expansion continuously to ensure plant survival. Therefore, it is of agricultural importance to study modulation of cellular expansion in roots upon distinct exogenous stimuli. The ability to modulate on subcellular level cell morphology and orchestrate cell expansion is evolutionary conserved and its accurate spatial and temporal regulation allows especially sessile plants to adjust and survive in an everchanging environment. To understand the impact of individual stimuli that are interfering with cell expansion modulation, and thereby with root movement patterns, we established an experimental setup that allows to grow roots under more controlled conditions. This includes growing roots shaded from direct root illumination, without exogenous sugar supplementation and including so-called root penetration assays to avoid unilateral mechanostimulus. We observed that this adapted growth conditions help immensely to reduce randomness of root growth adaptation, which both can mask or exaggerate mutant phenotypes. We showed recently that shootward auxin transport towards the elongation zone, orchestrated by the auxin influx carrier AUX1, is required to ensure directional root growth along the gravity vector by modulating a twisting movement at the elongation zone and by modulating root elongation rate. Furthermore, under the improved growth conditions, root bending response of gravistimulated roots is more uniformly performed among individual plants, compared to roots grown on sugar supplemented medium and exposed to direct illumination, which makes it easier to study cellular mechanoadaptation processes.

Improvement of plant growth conditions and live-cell imaging to track fast epidermal cell adjustments that underpin directional root growth control

Root cultivation adjustments allow to track cell morphology changes (mechanoadaptation) during gravitropic root response

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. Therefore, we investigate how cells adjust they properties upon gravitropic stimulus of Arabidopsis thaliana roots to initiate required curvature establishment at the lower part of the root. We grow roots shaded from light and without exogenous sucrose supplementation, to exclude unnecessary stimuli that would trigger random cell elongation processes, which allows us more uniform tracking of root bending by using a confocal microscope with vertical stage. First results show that gravitropic response requires epidermal cell file rotation starting at the very root tip towards the elongation zone, where in a neighboring cell file few cells alter their cell expansion to initiate the curvature during directional root growth adaptation.

NIP4:GFP marking epidermal cell plasma membrane
PIN2:GFP marking plasma membranes of cells in the root tip

Selected publications


Pree S, Malekian B, Sandén H, Nicolaisen M, Weckwerth W, Vestergård M, Retzer K. Deciphering the biological processes in root hairs required for N-self-fertilizing cereals. Front Plant Physiol [Internet]. 2023;1. Available from:

Vaňková R. et al. Responses to abiotic and biotic stresses – from the cellular level to fruit development – contributions of the Czech Centre for Experimental Plant Biology. Biologia Plantarum (2023) 67: 166-174,

Retzer K, Ibl V. Editorial: Highlights of the 2nd D(dark grown)-root meeting. Front Plant Sci. 2023 Jun 21;14:1227490.

Retzer K, Weckwerth W. Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems. Front Plant Sci. 2023 Mar 16;14:1154088.


Konstantinova, N.; Hörmayer, L.; Glanc, M.; Keshkeih, R.; Tan, S.; Di Donato, M.; Retzer, K.; Moulinier-Anzola, J.; Schwihla, M.; Korbei, B.; Geisler, M.; Friml, J.; Luschnig, C. WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions. Nat. Commun. 2022, 13 (1), 5147.

Retzer, K.; Moulinier-Anzola, J.; Lugsteiner, R.; Konstantinova, N.; Schwihla, M.; Korbei, B.; Luschnig, C. Endosomally Localized RGLG-Type E3 RING-Finger Ligases Modulate Sorting of  Ubiquitylation-Mimic PIN2. Int. J. Mol. Sci. 2022, 23 (12).

Kashkan, I.; García-González, J.; Lacek, J.; Müller, K.; Růžička, K.; Retzer, K.; Weckwerth, W. 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. bioRxiv 2022.

Retzer, K.: Continuous Tracking of Gravistimulated Roots in a Chambered Coverslip by Confocal Microscopy Allows First Glimpse on Mechanoadaptation of Cell Files during Curvature Initiation. bioRxiv 2022.

Starodubtseva, A.. et al. An Arabidopsis mutant deficient in phosphatidylinositol-4-phosphate kinases ß1 and ß2 displays altered auxin-related responses in roots. Sci. Rep. (2022)

García-González, J., Lacek, J., Weckwerth, W. & Retzer, K. Throttling Growth Speed: Evaluation of aux1-7 Root Growth Profile by Combining D-Root system and Root Penetration Assay. Plants 11, (2022).

Kashkan, I. et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated  tropic responses in Arabidopsis thaliana. New Phytol. 233, 329–343 (2022).


García-González, J., Lacek, J. & Retzer, K. Dissecting Hierarchies between Light, Sugar and Auxin Action Underpinning Root and Root Hair Growth. Plants (2021) doi:10.3390/plants10010111.

Lacek, J., García-González, J., Weckwerth, W. & Retzer, K. Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination. Int. J. Mol. Sci. 22, (2021).

García-González, J., Lacek, J., Weckwerth, W. & Retzer, K. Exogenous carbon source supplementation counteracts root and hypocotyl growth  limitations under increased cotyledon shading, with glucose and sucrose differentially modulating growth curves. Plant Signal. Behav. 1969818 (2021) doi:10.1080/15592324.2021.1969818.

Müller, K. et al. DIOXYGENASE FOR AUXIN OXIDATION 1 catalyzes the oxidation of IAA amino acid  conjugates. Plant Physiol. 187, 103–115 (2021).

Retzer, K. & Weckwerth, W. The Tor–Auxin connection upstream of root hair growth. Plants (2021) doi:10.3390/plants10010150.


Retzer, K. et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nat. Commun. (2019) doi:10.1038/s41467-019-13543-1.


Singh, G., Retzer, K., Vosolsobě, S. & Napier, R. Advances in understanding the mechanism of action of the auxin permease aux1. International Journal of Molecular Sciences (2018) doi:10.3390/ijms19113391.

Retzer, K., Singh, G. & Napier, R. M. It starts with TIRs. Nat. plants 4, 410–411 (2018).

Retzer, K. et al. Evolutionary conserved cysteines function as cis-acting regulators of arabidopsis PIN-FORMED 2 distribution. Int. J. Mol. Sci. (2017) doi:10.3390/ijms18112274.