ACORBA: Automated workflow to measure <i>Arabidopsis thaliana</i> root tip angle dynamics

Serre, Nelson B.C.; Fendrych, Matyáš

doi:10.1017/qpb.2022.4

Cited by 11 publications

(12 citation statements)

References 37 publications

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“…The gravitropic experiment was done as described 15 : a thin layer of growth medium (½ MS, 1% (w/v) sucrose in 1% plant agar, Duchefa) containing 5-day-old seedlings was placed into a 3D-printed microscopy chamber. The chamber was placed vertically on the vertical stage microscope for 45 minutes to recover.…”

Section: Methodsmentioning

confidence: 99%

The AFB1 auxin receptor controls the cytoplasmic auxin response pathway inArabidopsis thaliana

Dubey

Han

Stutzman

et al. 2023

Preprint

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The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFBs auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Here we show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, are essential and sufficient for its specific role in the rapid response. Substitution of the N-terminal region of AFB1 with that of TIR1 disrupts its distinct cytoplasm-enriched localization and activity in rapid root growth inhibition. Importantly, the N-terminal region of AFB1 is indispensable for auxin-triggered calcium influx which is a prerequisite for rapid root growth inhibition. Furthermore, AFB1 negatively regulates lateral root formation and transcription of auxin-induced genes, suggesting that it plays an inhibitory role in canonical auxin signaling. These results suggest that AFB1 may buffer the transcriptional auxin response while it regulates rapid changes in cell growth that contribute to root gravitropism.

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Section: Methodsmentioning

confidence: 99%

The AFB1 auxin receptor controls the cytoplasmic auxin response pathway inArabidopsis thaliana

Dubey

Han

Stutzman

et al. 2023

Preprint

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“…After 30 min for recovery (or 2 h for treatment), plates were turned 90° and imaged every 30 min. Analysis was done by Acorba software (Serre & Fendrych, 2022).…”

Section: Methodsmentioning

confidence: 99%

Auxin co‐receptor IAA17/AXR3 controls cell elongation in Arabidopsis thaliana root solely by modulation of nuclear auxin pathway

Kubalová,

Müller,

Dobrev

et al. 2024

New Phytologist

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Summary The nuclear TIR1/AFB‐Aux/IAA auxin pathway plays a crucial role in regulating plant growth and development. Specifically, the IAA17/AXR3 protein participates in Arabidopsis thaliana root development, response to auxin and gravitropism. However, the mechanism by which AXR3 regulates cell elongation is not fully understood. We combined genetical and cell biological tools with transcriptomics and determination of auxin levels and employed live cell imaging and image analysis to address how the auxin response pathways influence the dynamics of root growth. We revealed that manipulations of the TIR1/AFB‐Aux/IAA pathway rapidly modulate root cell elongation. While inducible overexpression of the AXR3‐1 transcriptional inhibitor accelerated growth, overexpression of the dominant activator form of ARF5/MONOPTEROS inhibited growth. In parallel, AXR3‐1 expression caused loss of auxin sensitivity, leading to transcriptional reprogramming, phytohormone signaling imbalance and increased levels of auxin. Furthermore, we demonstrated that AXR3‐1 specifically perturbs nuclear auxin signaling, while the rapid auxin response remains functional. Our results shed light on the interplay between the nuclear and cytoplasmic auxin pathways in roots, revealing their partial independence but also the dominant role of the nuclear auxin pathway during the gravitropic response of Arabidopsis thaliana roots.

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“…After 30 min for recovery (or 2h for treatment), plates were turned 90° and imaged every 30 minutes. Analysis was done by ACORBA software (Serre and Fendrych 2022).…”

Section: Methodsmentioning

confidence: 99%

“…After 30 min for recovery (or 2h for treatment), plates were turned 90° and imaged every 30 minutes. Analysis was done by ACORBA software (Serre and Fendrych 2022). The size of the meristematic and elongation zone was measured on roots stained with 2,5 μM PI for 15 min.…”

Section: Image Analyses and Measurementsmentioning

confidence: 99%

Auxin coreceptor IAA17/AXR3 controls cell elongation inArabidopsis thalianaroot by modulation of auxin and gibberellin perception

Kubalova

Müller

Dobrev

et al. 2023

Preprint

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The nuclear TIR1/AFB - Aux/IAA auxin pathway plays a crucial role in regulating plant growth and development. Specifically, the IAA17/AXR3 protein participates in root development, and the accumulation of its mutant variant, AXR3-1, which cannot bind auxin, leads to severe root growth phenotype and agravitropism. However, the mechanism by which AXR3 regulates cell elongation is not fully understood. Here we show that the inducible expression of AXR3-1 in the Arabidopsis thaliana root triggers excessive cell elongation that is followed by growth arrest of the root. We exploited this effect to reveal the underlying molecular mechanism of AXR3 action. We show that AXR3-1 acts exclusively in the nucleus where it interferes with the nuclear auxin transcriptional pathway, while the rapid cytoplasmic auxin root growth response is not affected. The analysis of the transcriptome of the induced AXR3-1 roots revealed changes in phytohormone perception and homeostasis. We show that the accumulation of AXR3-1 disturbs auxin homeostasis which leads to excessive auxin accumulation. At the same time, the reaction of the AXR3-1 roots to gibberellin is altered. These results show that the IAA17/AXR3 maintains an optimal cell elongation rate by controlling the auxin response, auxin homeostasis and the interplay with gibberellin signaling.

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ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamics

Cited by 11 publications

References 37 publications

The AFB1 auxin receptor controls the cytoplasmic auxin response pathway inArabidopsis thaliana

The AFB1 auxin receptor controls the cytoplasmic auxin response pathway inArabidopsis thaliana

Auxin co‐receptor IAA17/AXR3 controls cell elongation in Arabidopsis thaliana root solely by modulation of nuclear auxin pathway

Auxin coreceptor IAA17/AXR3 controls cell elongation inArabidopsis thalianaroot by modulation of auxin and gibberellin perception

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