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Biology subjects

Jones, A. M.

Publications and source records attributed to Jones, A. M..

At least 19 recordsLinked to original sources
bioRxiv2025

UDP-glucose Activation of a G-protein/Sucrose Synthase Signaling Supercomplex

Arabidopsis thaliana REGULATOR OF G PROTEIN SIGNALING 1 (AtRGS1, hereafter, RGS1) within the heterotrimeric G protein complex plays a role in sensing extracellular signals. High millimolar concentrations of some sugars induce RGS1 endocytosis and therefore G protein activation. However, this is not likely a direct, rather an indirect effect through a sugar metabolite. One metabolite at the plasma membrane where RGS1 resides is UDP-glucose (UDPG) produced by SUCROSE SYNTHASE (SUS) enzymes, previously shown to interact with RGS1. Our direct measurements indicate that the Kd for UDPG binding to RGS1 (2.4 {micro}M) is consistent with UDPG activation of RGS1 with an EC50 of 17 {micro}M to rapidly trigger G protein activation within minutes. RGS1 associates directly with SUS1 and SUS4, exhibiting affinities (Kd = 161 nM and 106 nM, respectively) that are markedly tighter than the corresponding Km values for UDPG formation (40 {micro}M and 70 {micro}M, respectively). Therefore, SUS may be one source for this RGS1 ligand in a manner analogous to "metabolite funneling" in enzymology. UDPG induces rapid phosphorylation of RGS1 at the C-terminal phosphorylation cluster, a site previously implicated in RGS1 endocytosis and G protein activation. UDPG activation of RGS1 changes the global transcript profiles in various processes, largely involving plant defense. These results provide the first molecular evidence for UDPG as a newly recognized low-molecular weight signal controlling key aspects of plant physiology.

plant biology↗
bioRxiv2025

A balance of metabolism and diffusion articulates a gibberellin hormone gradient in the Arabidopsis root

The plant hormone gibberellin (GA4) regulates numerous developmental processes. Within the root, GA4 controls growth, in part, by controlling the extent of cell elongation. The nlsGPS1 FRET biosensor revealed a GA4 gradient within the Arabidopsis root growth zones, with GA4 levels correlating with cell length. We developed a multiscale mathematical model to understand how biosynthesis, catabolism and transport create the GA4 distribution within the root growth zones. The model showed that phloem delivery of the biosynthetic intermediate GA12 contributes to higher levels of bioactive GA4 in the elongation zone, with the GA4 synthesis pattern being further modified by local GA12 synthesis in the quiescent centre region and the spatial distribution of biosynthesis enzymes (GA20ox and GA3ox). Model predictions revealed that whilst GA20ox and GA3ox transcript is present throughout the growth zones, these enzymes are inactive in the dividing cells, which explains steep GA4 gradients observed in GA20ox and GA3ox over-expression lines, and improves agreement between model predictions and data in wildtype, ga20ox and ga3ox lines. The model revealed that the GA4 gradient also depends a balance of diffusion through plasmodesmata and catabolism. Both model predictions and biosensor data demonstrated that plasmodesmatal diffusion enables a more gradual GA4 gradient, with higher diffusion antagonizing the GA4 gradient. Model predictions suggested that catabolism limits GA4 levels, which we validated via biosensor imaging in the ga2oxhept mutant. We concluded that GA4 distribution mediates root growth programming via local GA4 synthesis combining with diffusion and catabolism to create a spatial gradient that provides positional information and patterns cell elongation.

plant biology↗
bioRxiv2025

Gibberellin-deactivating GA2OX enzymes act as a hub for auxin-gibberellin crosstalk in Arabidopsis thaliana root growth regulation

Plant bodies are built from immobile cells, making the regulation of cell expansion essential for growth, development, and adaptation. In roots, cell elongation executes the movement of the root tips through soil. This process is tightly controlled by numerous signaling pathways. Among these, gibberellin and auxin signaling stand out for their contrasting effects on root growth, interacting through complex crosstalk at multiple regulatory levels. Here we reveal the molecular basis of the auxin-gibberellin crosstalk in the model plant Arabidopsis thaliana. We show that auxin signaling pathway steers the expression of GIBBERELLIN 2-OXIDASES (GA2OX), key gibberellin-deactivating enzymes in the root elongation zone. GA2OX are negative regulators of root cell elongation; GA2OX8 overexpression decreases gibberellin levels and inhibits root cell elongation, in contrast, the ga2ox heptuple mutant roots show elevated gibberellin levels in the elongation zone and grow longer roots. Shoot derived auxin can regulate GA2OX8 expression in roots, linking systemic auxin signaling to local gibberellin modulation. In addition, GA2OX8 is active in vascular tissues and the stem cell niche, tissues with high auxin levels. Loss of GA2OX genes results in altered stem cell niche, including increased quiescent center size and expanded root cell layers, highlighting the role of these enzymes in maintaining tissue organization. Together, our findings identify GA2OX6 and GA2OX8 enzymes as key mediators of auxin-gibberellin crosstalk, providing insights into their roles in root elongation, vascular development, and stem cell niche maintenance. These results expand our understanding of how auxin integrates with gibberellin signaling to coordinate root development and growth dynamics.

plant biology↗
bioRxiv2023

Comparing hormone dynamics in cereal crops via transient expression of hormone sensors

Plant hormones are small molecules which elicit profound physiological responses. Although plant hormone biosynthesis and response genes have been critical for agricultural improvement, it has been difficult to experimentally compare hormone biology across species because of complex phenotypic outputs. We used transient expression of genetic hormone sensors and transcriptomics to quantify tissue-specific gibberellic acid (GA) and auxin responses across tissues and genotypes in cereal crops. We found that the FRET-based GPS2 biosensor detects exogenous GA treatments in maize, barley, sorghum, and wheat, in both vegetative and floral tissues. Measuring GPS2 output across GA dosages revealed tissue- and genotype-specific differences in GA sensor response. We observed marked differences in maize vs barley leaves and floral tissues and an unexpected drop in GPS2 output in the maize d1 GA biosynthesis mutant after GA treatment, likely reflecting differences in bioactive GA content, GA transport, and mechanisms of GA response. We then used RNAseq to measure transcriptional responses to GA treatment in leaves from maize wildtype, d1, and barley as well as floral tissues from maize and barley for a cross-tissue, cross-genotype, and cross-species GA-response comparison. After orthology prediction and analysis of within- and cross-species GO-term enrichment, we identified core sets of GA-responsive genes in each species as well as maize- barley orthogroups. Our analysis suggests that downregulation of GA-INSENSITIVE DWARF1 (GID1) and upregulation of -Expansin1 (EXPA1) orthologs comprises a universal GA-response mechanism that is independent of GA biosynthesis, and identifies F-Box proteins, hexokinase, and AMPK/SNF1 protein kinase orthologs as unexpected cross-tissue, cross-genotype, and cross-species GA-responsive genes. We then compared the transient expression of the DR5, DR5v2, and DII-mDII auxin reporters in barley and maize and find that although DR5 did not respond to exogenous auxin in barley, DR5v2 responded to auxin treatment with a similar magnitude as in maize. Both species display auxin-mediated DII degradation that requires the 26S proteasome.

plant biology↗
bioRxiv2023

Gibberellin Perception Sensors 1 and 2 reveal cellular GA dynamics articulated by COP1 and GA20ox1 that are necessary but not sufficient to pattern hypocotyl cell elongation

The phytohormone gibberellin (GA) is critical for environmentally sensitive plant development including germination, skotomorphogenesis and flowering. The FRET biosensor GIBBERELLIN PERCEPTION SENSOR1, which permits single-cell GA measurements in vivo, was previously used to observe a GA gradient correlated with cell length in dark-grown but not light-grown hypocotyls. We sought to understand how light signalling integrates into cellular GA regulation. Here we show how the E3 ligase COP1 and transcription factor HY5 play central roles in directing cellular GA distribution in skoto- and photomorphogenic hypocotyls, respectively. We demonstrate that the expression pattern of biosynthetic enzyme GA20ox1 is the key determinant of the GA gradient in dark-grown hypocotyls and is a target of COP1 signalling. We engineered a second generation GPS2 biosensor with improved orthogonality and reversibility to show the cellular pattern of GA depletion during the transition to growth in the light. This GA depletion partly explains the resetting of hypocotyl growth dynamics during photomorphogenesis. Achieving cell-level resolution has revealed how GA distributions link environmental conditions with morphology and morphological plasticity and the GPS2 biosensor is an ideal tool for GA studies in further conditions, organs and plant species.

plant biology↗
bioRxiv2023

Stomata, a vulnerability in the plant defence against phytophagous mites that ABA can overcome

Arthropod herbivory possess a significant threat to crop yield, prompting plants to employ intricate defense mechanisms against pest feeding. The generalist pest, Tetranychus urticae, inflicts rapid damage and remains a challenge due to its broad target range. In this study, we explored Arabidopsis thalianas response to T. urticae infestation, revealing the induction of abscisic acid (ABA), a hormone typically associated with abiotic stress adaptation, including stomatal closure during water stress. Leveraging a FRET-based ABA biosensor (nlsABACUS2-400n), we observed elevated ABA levels in various leaf cell types post-mite feeding. While ABAs role in pest resistance or susceptibility has been debated, an ABA-deficient mutant exhibited increased mite infestation, alongside intact canonical biotic stress signalling, indicating an independent function of ABA in mite defense. Through genetic and pharmacological interventions targeting ABA levels, ABA signalling, stomatal aperture, and density, we established that ABA-triggered stomatal closure effectively hinders mite feeding and minimizes leaf cell damage. This study underscores the critical interplay between biotic and abiotic stresses in plants, highlighting how the vulnerability to mite infestation arising from open stomata, crucial for transpiration and photosynthesis, underscores the intricate relationship between these two stress types.

plant biology↗
bioRxiv2023

Cellular gibberellin dynamics govern indeterminate nodule development, morphologyand function

During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determined the cellular location and function of bioactive GA during nodule organogenesis using a genetically-encoded second generation GA biosensor, GPS2. We found endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions and maintaining accumulation in the mature nodule meristem. We show, through mis-expression of GA catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that cytokinin as well as nodule-identity genes induce and sustain GA accumulation necessary for nodule function.

plant biology↗
bioRxiv2023

Auxin coreceptor IAA17/AXR3 controls cell elongation in Arabidopsis thaliana root by modulation of auxin and gibberellin perception

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.

plant biology↗
bioRxiv2022

Highlighter: an optogenetic actuator for light-mediated, high resolution gene expression control in plants

Optogenetic actuators have revolutionized the resolution at which we can assert control over biological processes in living systems. In plants, deployment of optogenetics is challenging due to the need for these light-responsive systems to maintain a single activation state in conventional horticultural environments with light-dark cycling. Furthermore, many available optogenetic actuators are based on plant photoreceptors that might crosstalk with endogenous signaling processes, while others depend on exogenously supplied cofactors. To overcome such challenges, we have developed Highlighter; a synthetic, light-gated gene expression system tailored for in planta function. Highlighter is based on the photoswitchable CcaS-CcaR system from cyanobacteria and is repurposed for plants as a fully genetically encoded system, engineered to photoswitch with the endogenous plant chromophore, phytochromobilin. We deployed Highlighter in transiently transformed Nicotiana benthamiana for optogenetic control of fluorescent protein expression and innate immune responses. Using light to guide differential fluorescent protein expression in nuclei of neighboring cells, we demonstrate unprecedented spatiotemporal control of target gene expression. We furthermore regulate activation of plant immunity by modulating the spectral composition of white light, demonstrating optogenetic control of a biological process in horticultural light environments. Highlighter is a step forward for optogenetics in plants and a technology for high-resolution gene induction that will advance fundamental plant biology and provide new opportunities for crop improvement.

synthetic biology↗
bioRxiv2022

Next-generation ABACUS biosensors reveal cellular ABA dynamics driving root growth at low aerial humidity

The plant hormone abscisic acid (ABA) accumulates under abiotic stress to recast water relations and development. To overcome a lack of high-resolution, sensitive reporters, we developed ABACUS2s, next-generation FRET biosensors for ABA with high affinity, signal-to-noise ratio and orthogonality, that reveal endogenous ABA patterns in Arabidopsis thaliana. We mapped stress-induced ABA dynamics in high-resolution to reveal the cellular basis for local and systemic ABA functions. At reduced foliar humidity, roots cells accumulated ABA in the elongation zone, the site of phloem transported ABA unloading. Phloem ABA and root ABA signalling were both essential to maintain root growth at low humidity. ABA coordinates a robust system to maintain root growth in response to foliar stresses, enabling plants to maintain foraging of deeper soil for water uptake

plant biology↗
bioRxiv2022

ABA signaling prevents phosphodegradation of the Arabidopsis SR45 splicing factor to negatively autoregulate inhibition of early seedling development

Alternative splicing is a key posttranscriptional mechanism to expand the coding capacity of eukaryotic genomes. Although the functional relevance of this process remains poorly understood in plant systems, major modulators of alternative splicing called serine/arginine-rich (SR) proteins have been implicated in plant stress responses mediated by the abscisic acid (ABA) hormone. Loss of function of the Arabidopsis thaliana SR-like protein SR45, a bona fide splicing factor, has been shown to cause plant hypersensitivity to environmental cues and activation of the ABA pathway. Also, consistent with both animal and plant SR proteins being extensively and reversibly phosphorylated at their C-termini, ABA-induced changes in the phosphorylation status of SR45 have been reported. Here, we show that SR45 overexpression reduces Arabidopsis sensitivity to ABA during early seedling development. Moreover, exposure to ABA dephosphorylates SR45 at multiple amino acid residues and leads to accumulation of the protein via reduction of SR45 ubiquitination and proteasomal degradation. Using phosphomutant and phosphomimetic transgenic Arabidopsis lines, we demonstrate the functional relevance of ABA-mediated dephosphorylation of a single SR45 residue, T264, in antagonizing SR45 ubiquitination and degradation to promote its function as a repressor of seedling ABA sensitivity. Taken together, our results reveal a mechanism in which ABA signaling negatively autoregulates during early plant development via posttranslational control of the SR45 splicing factor.

plant biology↗
bioRxiv2021

Phosphorylation dynamics in a flg22 induced, heterotrimeric G protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking

flg22 is a 22-amino peptide released from bacterial flagellin, a Microbe-Associated Molecular Pattern (MAMP) that is recognized by the plant cell as a signal indicating that bacteria are present. On its own, flg22 initiates a rapid increase in cytoplasmic calcium, extracellular reactive oxygen species, and activation of a Mitogen Activated Protein Kinase (MAPK) cascade, all of which are activated within 15 minutes after the cell perceives flg22. Here we show a massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome within this 15-minute duration in wildtype and a mutant deficient in G-protein coupled signaling. Integration of phosphoproteome with protein-protein interactome data followed by network topology analyses discovered that many of the flg22-induced phosphoproteome changes fall on proteins that comprise the G protein interactome and on the most highly populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the G-protein interactome depend on a functional heterotrimeric G protein complex, some occur on proteins that interact directly with components of G-coupled signal transduction. One of these is ATB, a substrate-recognition sub-unit of the PP2A Ser/Thr phosphatase and an interactor to Arabidopsis thaliana REGULATOR OF G SIGNALING 1 protein (AtRGS1), a 7-transmembrane spanning modulator of the nucleotide-binding state of the core G protein complex. AtRGS1 is phosphorylated by BAK1, a component of the flg22 receptor, to initiate AtRGS1 endocytosis. A null mutation of ATB confers high basal endocytosis of AtRGS1, suggesting sustained phosphorylated status. Loss of ATB confers traits associated with loss of AtRGS1. Because the basal level of AtRGS1 is lower in the atb null mutant in a proteasome-dependent manner, we propose that phosphorylation-dependent endocytosis of AtRGS1 is part of a mechanism to degrade AtRGS1 which then sustains activation of the G protein complex. Thus, the role of ATB is now established as a central component of phosphorylation-dependent regulation of system dynamics in innate immunity.

systems biology↗
bioRxiv2021

A quantitative gibberellin signalling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem

Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signalling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this novel degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signalling activity in the SAM. We show that high GA signalling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organisation of internodes, thus contributing to internode specification in the SAM.

plant biology↗
bioRxiv2021

A Model for Self-Organization of Sensorimotor Function: The Spinal Monosynaptic Loop

Recent spinal cord literature abounds with descriptions of genetic preprogramming and the molecular control of circuit formation. In this paper we explore to what extent circuit formation based on learning rather than preprogramming could explain some prominent aspects of the spinal cord connectivity patterns observed in animals. To test this we developed an artificial organism with a basic musculoskeletal system and proprioceptive sensors, connected to a neural network. We adjusted the initially randomized gains in the neural network according to a Hebbian plasticity rule while exercising the model system with spontaneous muscle activity patterns similar to those observed during early fetal development. The resulting connection matrices support functional self-organization of the mature pattern of Ia to motoneuron connectivity in the spinal circuitry. More coordinated muscle activity patterns such as observed later during neonatal locomotion impaired projection selectivity. These findings imply a generic functionality of a musculoskeletal system to imprint important aspects of its mechanical dynamics onto a neural network, without specific preprogramming other than setting a critical period for the formation and maturation of this general pattern of connectivity. Such functionality would facilitate the successful evolution of new species with altered musculoskeletal anatomy and it may help to explain patterns of connectivity and associated reflexes that appear during abnormal development.

neuroscience↗
bioRxiv2021

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Methods that dynamically monitor these intracellular effects are currently lacking. Here, we leveraged the environmental sensitivity and structural plasticity of intrinsically disordered regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use in environmentally-responsive molecular tools.

cell biology↗
bioRxiv2020

Evolutionarily ancient role of cholecystokinin-type neuropeptide signalling as an inhibitory regulator of feeding-related processes revealed in an echinoderm

Cholecystokinin (CCK) / sulfakinin (SK)-type neuropeptides regulate feeding and digestion in chordates and protostomes (e.g. insects). Here we characterised CCK/SK-type signalling for the first time in a non-chordate deuterostome - the starfish Asterias rubens (phylum Echinodermata). In this species, two neuropeptides (ArCCK1, ArCCK2) derived from the precursor protein ArCCKP act as ligands for a CCK/SK-type receptor (ArCCKR) and are expressed in the nervous system, digestive system, tube feet and body wall. Furthermore, ArCCK1 and ArCCK2 cause dose-dependent contraction of cardiac stomach, tube foot and body wall apical muscle preparations in vitro and injection of these neuropeptides in vivo triggers cardiac stomach retraction and inhibition of the onset of feeding in A. rubens. Thus, an evolutionarily ancient role of CCK/SK-type neuropeptides as inhibitory regulators of feeding-related processes in the Bilateria has been conserved in the unusual and unique context of the extra-oral feeding behaviour and pentaradial body plan of an echinoderm.

physiology↗
bioRxiv2020

Molecular switch architecture drives response properties

Many intracellular signaling pathways are composed of molecular switches, proteins that transition between two states--on and off. Typically, signaling is initiated when an external stimulus activates its cognate receptor that in turn causes downstream switches to transition from off to on using one of the following mechanisms: activation, in which the transition rate from the off state to the on state increases; derepression, in which the transition rate from the on state to the off state decreases; and concerted, in which activation and derepression operate simultaneously. We use mathematical modeling to compare these signaling mechanisms in terms of their dose-response curves, response times, and abilities to process upstream fluctuations. Our analysis elucidates several general principles. First, activation increases the sensitivity of the pathway, whereas derepression decreases sensitivity. Second, activation generates response times that decrease with signal strength, whereas derepression causes response times to increase with signal strength. These opposing features allow the concerted mechanism to not only show dose-response alignment, but also to decouple the response time from stimulus strength. However, these potentially beneficial properties come at the expense of increased susceptibility to up-stream fluctuations. In addition to above response metrics, we also examine the effect of receptor removal on switches governed by activation and derepression. We find that if inactive (active) receptors are preferentially removed then activation (derepression) exhibits a sustained response whereas derepression (activation) adapts. In total, we show how the architecture of molecular switches govern their response properties. We also discuss the biological implications of our findings.

systems biology↗