Dissecting the molecular mechanism regulating lateral root hydropatterning

Lateral roots (LR) contribute considerably to the architecture of the root system. The hormone auxin tightly controls the regulation of LR formation in response to environmental signals. For example, roots have the ability to distinguish between wet and dry micro environments in the soil and adapt the positioning of lateral roots accordingly. This concept is referred to as LR hydropatterning and is a novel adaptive mechanism for controlling root branching. When growing vertically down an agar plate, Arabidopsis thaliana roots are also exposed to an asymmetric distribution of water that causes a meniscus to form around the primary root (PR) circumference. LRs develop preferentially on the side of the PR in contact with water, rather than the side exposed to air. My project aims to elucidate the underlying molecular mechanisms controlling this novel adaptive response. It has been revealed that the transcription factor AUXIN RESPONSE FACTOR 7 (ARF7) is essential for LR hydropatterning. In contrast to wild type, arf7 loss of function mutants do not exhibit greater LR emergence on the side of the PR in contact with moisture. Ectopic expression of ARF7 (in 35S:ARF7 arf7-1) can rescue arf7 LR hydropatterning, implying that ARF7 regulates LR hydropatterning via a post-transcriptional mechanism. One promising post-transcriptional mechanism that may control LR hydropatterning involves protein SUMOylation (a Small Ubiquitin-like Modifier), since the SUMO mutant ots1 ots2 phenocopies the arf7 LR hydropatterning defect. OTS1 and OTS2 encode nuclear localised proteases that remove SUMO from target proteins. ARF7 is a target for SUMO modification, containing several SUMOylation sites including one within its DNA binding domain. Expressing wild type ARF7 and a non-SUMOylated version in arf7 revealed that ARF7 controls LR hydropatterning via SUMOylation. This knowledge will help reveal how plants explore the soil and position LR to maximise water (and nutrient) foraging

Arabidopsis antibody resources for functional studies in plants

© 2020, The Author(s). Here we report creation of a unique and a very valuable resource for Plant Scientific community worldwide. In this era of post-genomics and modelling of multi-cellular systems using an integrative systems biology approach, better understanding of protein localization at sub-cellular, cellular and tissue levels is likely to result in better understanding of their function and role in cell and tissue dynamics, protein–protein interactions and protein regulatory networks. We have raised 94 antibodies against key Arabidopsis root proteins, using either small peptides or recombinant proteins. The success rate with the peptide antibodies was very low. We show that affinity purification of antibodies massively improved the detection rate. Of 70 protein antibodies, 38 (55%) antibodies could detect a signal with high confidence and 22 of these antibodies are of immunocytochemistry grade. The targets include key proteins involved in hormone synthesis, transport and perception, membrane trafficking related proteins and several sub cellular marker proteins. These antibodies are available from the Nottingham Arabidopsis Stock Centre

Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy

Studying the developmental genetics of plant organs, requires following gene expression in specific tissues. To facilitate this, we have developed the Dual Expression Anatomy Lines (DEAL), which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24h,. and cCoupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin

Hydraulic flux–responsive hormone redistribution determines root branching

Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution

Dissecting the molecular mechanism regulating lateral root hydropatterning

Lateral roots (LR) contribute considerably to the architecture of the root system. The hormone auxin tightly controls the regulation of LR formation in response to environmental signals. For example, roots have the ability to distinguish between wet and dry micro environments in the soil and adapt the positioning of lateral roots accordingly. This concept is referred to as LR hydropatterning and is a novel adaptive mechanism for controlling root branching. When growing vertically down an agar plate, Arabidopsis thaliana roots are also exposed to an asymmetric distribution of water that causes a meniscus to form around the primary root (PR) circumference. LRs develop preferentially on the side of the PR in contact with water, rather than the side exposed to air. My project aims to elucidate the underlying molecular mechanisms controlling this novel adaptive response. It has been revealed that the transcription factor AUXIN RESPONSE FACTOR 7 (ARF7) is essential for LR hydropatterning. In contrast to wild type, arf7 loss of function mutants do not exhibit greater LR emergence on the side of the PR in contact with moisture. Ectopic expression of ARF7 (in 35S:ARF7 arf7-1) can rescue arf7 LR hydropatterning, implying that ARF7 regulates LR hydropatterning via a post-transcriptional mechanism. One promising post-transcriptional mechanism that may control LR hydropatterning involves protein SUMOylation (a Small Ubiquitin-like Modifier), since the SUMO mutant ots1 ots2 phenocopies the arf7 LR hydropatterning defect. OTS1 and OTS2 encode nuclear localised proteases that remove SUMO from target proteins. ARF7 is a target for SUMO modification, containing several SUMOylation sites including one within its DNA binding domain. Expressing wild type ARF7 and a non-SUMOylated version in arf7 revealed that ARF7 controls LR hydropatterning via SUMOylation. This knowledge will help reveal how plants explore the soil and position LR to maximise water (and nutrient) foraging

Uncovering How Auxin Optimizes Root Systems Architecture in Response to Environmental Stresses

Since colonizing land, plants have developed mechanisms to tolerate a broad range of abiotic stresses that include flooding, drought, high salinity, and nutrient limitation. Roots play a key role acclimating plants to these as their developmental plasticity enables them to grow toward more favorable conditions and away from limiting or harmful stresses. The phytohormone auxin plays a key role translating these environmental signals into developmental outputs. This is achieved by modulating auxin levels and/or signaling, often through cross talk with other hormone signals like abscisic acid (ABA) or ethylene. In our review, we discuss how auxin controls root responses to water, osmotic and nutrient-related stresses, and describe how the synthesis, degradation, transport, and response of this key signaling hormone helps optimize root architecture to maximize resource acquisition while limiting the impact of abiotic stresses

Turning up the volume: How root branching adaptive responses aid water foraging

Access to water is critical for all forms of life. Plants primarily access water through their roots. Root traits such as branching are highly sensitive to water availability, enabling plants to adapt their root architecture to match soil moisture distribution. Lateral root adaptive responses hydropatterning and xerobranching ensure new branches only form when roots are in direct contact with moist soil. Root traits are also strongly influenced by atmospheric humidity, where a rapid drop leads to a promotion of root growth and branching. The plant hormones auxin and/or abscisic acid (ABA) play key roles in regulating these adaptive responses. We discuss how these signals are part of a novel “water-sensing” mechanism that couples hormone movement with hydrodynamics to orchestrate root branching responses

Root branching toward water involves posttranslational modification of transcription factor ARF7

Plants adapt to heterogeneous soil conditions by altering their root architecture. For example, roots branch when in contact with water using the hydropatterning response. We report that hydropatterning is dependent on auxin response factor ARF7. This transcription 5 factor induces asymmetric expression of its target gene LBD16 in lateral root founder cells on the side of the root in contact with water. This differential expression pattern is regulated by post-translational modification of ARF7 with the SUMO protein. SUMOylation negatively regulates ARF7 DNA binding activity. ARF7 SUMOylation is required to recruit the Aux/IAA repressor protein IAA3. Blocking ARF7 SUMOylation disrupts IAA3 10 recruitment and hydropatterning. We conclude that SUMO-dependent regulation of auxin response controls root branching pattern in response to water availability

Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

The original version of this Article omitted the following from the Acknowledgements: ‘We also thank DBT-CREST BT/HRD/03/01/2002.’ This has been corrected in both the PDF and HTML versions of the Article