Biology subjects

Novak, O.

Publications and source records attributed to Novak, O..

72 records · Page 4Linked to original sources

bioRxiv2020

A role of DAO1 in oxidation of IAA amino acid conjugates revealed through metabolite, high throughput transcript and protein level analysis.

Auxin metabolism is, together with auxin transport, a key determinant of auxin signalling output in plant cells, yet details on the underlying mechanisms and factors involved are still largely unknown. Processes involved in the auxin metabolism are subject to regulation based on numerous signals, including auxin concentration itself. Altered auxin availability and the subsequent changes of auxin metabolite profiles can therefore elucidate the function and regulatory role of individual elements in the auxin metabolic machinery. After analysing auxin metabolism in auxin dependent tobacco BY-2 cell line grown in presence or absence of synthetic auxin 2,4-D we found that both conditions were similarly characterized by very low levels of endogenous indole-3-acetic acid (IAA) and its metabolites. However, metabolic profiling after exogenous application of IAA uncovered that the concentration of N-(2-oxindole-3-acetyl)-L-aspartic acid (oxIAA-Asp), the most abundantly formed auxin metabolite in the control culture, dramatically decreased in auxin-starved conditions. To describe the molecular mechanism behind this regulation, we analysed transcriptome and proteome changes caused by auxin starvation. While no changes in the expression of auxin biosynthetic machinery were observed, many genes related to auxin conjugation and degradation showed differential expression. Selected putative auxin glycosylating enzymes as well as members of the Gretchen Hagen 3 gene family involved in auxin amino acid conjugation showed both up- and down-regulation. Contrarily to that, all tobacco homologs of Arabidopsis thaliana DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), known to be responsible for the formation of oxIAA from IAA, showed significant downregulation at both transcript and protein levels. To validate the role of DAO1 in auxin metabolism, we performed auxin metabolite profiling in BY-2 mutants carrying either siRNA-silenced or CRISPR-Cas9-mutated NtDAO1, as well as in dao1-1 Arabidopsis thaliana plants. Both mutants showed not only expectedly lower levels of oxIAA, but also significantly lower abundance of oxidated amino acid conjugates of IAA (oxIAA-Asp). Our results thus represent the first direct evidence on DAO1 activity on IAA amino acid conjugates. Statement of significanceHere we present an analysis of auxin metabolism on metabolite, transcript and protein levels in tobacco BY-2 cell line, collectively identifying oxidation of IAA amino acid conjugates as a new role of DIOXYGENASE FOR AUXIN OXIDATION 1 within an auxin-level-responsive metabolic system.

plant biology↗

bioRxiv2020

The auxin transporter PIN1 and the cytokinin transporter AZG1 interact to regulate the root stress response

Root system development is crucial for optimal growth and yield in plants, especially in sub-optimal soil conditions. The architecture of a root system is environmentally responsive, enabling the plant to exploit regions of high nutrient density whilst simultaneously minimizing abiotic stress. Despite the vital contribution of root systems to the growth of both model and crop species, we know little of the mechanisms which regulate their architecture. One factor which is relatively well understood is the transport of auxin, a plant growth regulator which defines the frequency of lateral root (LR) initiation and the rate of LR outgrowth. Here we describe a search for proteins which regulate RSA by interacting directly with a key auxin transporter, PIN1. The native separation of PIN1 identified several co-purifying proteins. Among them, AZG1 was subsequently confirmed as a PIN1 interactor. AZG1-GFP fusions co-localized with PIN1 in procambium cells of the root meristem. Roots of azg1 plants contained less PIN1 and blocking proteolysis restored PIN1 levels, observations which are consistent with PIN1 being stabilized by AZG1 in the plasma membrane. Furthermore, we show that AZG1 is a cytokinin import protein; accordingly, azg1 plants are insensitive to exogenously applied cytokinin. In wild-type plants, the frequency of LRs falls with increasing salt concentration, a response which is not observed in azg1 x azg2 plants, although their drought response is unimpaired. This report therefore identifies a potential point for auxin:cytokinin crosstalk in the environmentally-responsive determination of root system architecture.

plant biology↗

bioRxiv2020

Light controls de novo adventitious root regeneration by modulating jasmonate and cytokinin homeostasis in Norway spruce hypocotyls

Vegetative propagation relies on the capacity of plants to regenerate de novo adventitious roots (ARs), a quantitative trait controlled by the interaction of endogenous factors such as hormones and environmental cues among which light plays a central role. However, the physiological and molecular components mediating light cues during AR initiation (ARI) remain largely elusive. We explored the effect of light spectral quality on ARI in de-rooted Norway spruce seedlings as well as on hormone metabolism with sensitive mass spectrometry-based methods. We coupled this to gene expression analysis to identify potential signaling pathways and to extensive anatomical characterization to investigate ARI at the cellular level. We showed that in contrast to white light and blue light, red light promoted ARI likely by reducing jasmonate (JA) and JA-isoleucine biosynthesis and repressing the accumulation of isopentyl-adenine-type cytokinins and abscisic acid. We confirmed that exogenously applied JA and/or CK inhibit ARI, and found that they possibly act in the same pathway. The negative effect of JA was confirmed at the histological level. We showed that JA represses the early events of ARI. In conclusion, RL promotes ARI by repressing the accumulation of the wound-induced phytohormones JA and CK. HighlightBlue and red light have an opposite effect on adventitious root initiation in Norway spruce hypocotyl, red light having a promoting effect by modulating hormone homeostasis.

plant biology↗

bioRxiv2020

A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies

Here we design and optimize a genetically encoded fluorescent indicator, iAChSnFR, for the ubiquitous neurotransmitter acetylcholine, based on a bacterial periplasmic binding protein. iAChSnFR shows large fluorescence changes, rapid rise and decay kinetics, and insensitivity to most cholinergic drugs. iAChSnFR revealed large transients in a variety of slice and in vivo preparations in mouse, fish, fly and worm. iAChSnFR will be useful for the study of acetylcholine in all animals.

neuroscience↗

bioRxiv2019

Cytokinin induction by the Jasmonate-induced AP2/ERF115 represses adventitious rooting in Arabidopsis

Jasmonate (JA), an oxylipin-derived phytohormone, plays crucial roles not only in plant immunity and defense against herbivorous insects but also in plant growth and developmental processes, including regeneration and organogenesis. However, the mechanistic basis of its mode of action and precise role in integrating other signaling cues are poorly understood. Here we provide genetic evidences that JA signaling acts in both NINJA-dependent and -independent modulation of the transcriptional activity of MYC transcription factors involved in the inhibition of adventitious root initiation (ARI). Our data show that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Moreover, transcriptomic comparison of ninja-1myc2-322B double mutant (which produce extremely few ARs) and wild type seedlings identified a novel molecular network governed by the APETALA2/ETHYLENE RESPONSE FACTOR 115 (ERF115) transcription factor. We demonstrate that JA-induced ERF115 activates the cytokinin signaling machinery and thereby represses ARI. Altogether, our results reveal a molecular network involving cooperative crosstalk between JA and CK machineries that inhibits ARI.

plant biology↗

bioRxiv2019

Cytokinin fluoroprobe and receptor CRE1/AHK4 localize to both plasma membrane and endoplasmic reticulum

The plant hormone cytokinin regulates various cell and developmental processes, including cell division and differentiation, embryogenesis, activity of shoot and root apical meristems, formation of shoot and root lateral organs and others 1. Cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Based on the subcellular localization of cytokinin receptors in various transient expression systems, such as tobacco leaf epidermal cells, and membrane fractionation experiments of Arabidopsis and maize, the endoplasmic reticulum (ER) membrane has been proposed as a principal hormone perception site 2-4. Intriguingly, recent study of the cytokinin transporter PUP14 has pointed out that the plasma membrane (PM)-mediated signalling might play an important role in establishment of cytokinin response gradients in various plant organs 5. However, localization of cytokinin HK receptors to the PM, although initially suggested 6, remains ambiguous. Here, by monitoring subcellular localizations of the fluorescently labelled natural cytokinin probe iP-NBD 7 and the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin fluoroprobes and receptors can enter the secretory pathway and reach the PM. We demonstrate that in cells of the root apical meristem, CRE1/AHK4 localizes to the PM and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. Our results provide a new perspective on cytokinin signalling and the possibility of multiple sites of perception at PM and ER, which may determine specific outputs of cytokinin signalling.

plant biology↗

bioRxiv2019

Cell-surface receptors enable perception of extracellular cytokinins

Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience 1,2. Although cytokinin receptors are substantially localised to the endoplasmic reticulum 3-5, the cellular sites of cytokinin perception continue to be debated 1,6,7. Several cytokinin types display bioactivity 8,9 and recently a cell-specific cytokinin gradient was reported in roots 10. Yet, the importance of spatially heterogeneous cytokinin distribution and the specific cytokinin(s) that account for the different responses remain unclear. Here we show that cytokinin perception by plasma membrane receptors is an effective path for cytokinin response in root cells. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP;11) is closely matched to intracellular cytokinin content, yet a proportion of bioactive cytokinins are detected in the extracellular fluid. Using cytokinins covalently linked to beads that could not pass the plasma membrane, we demonstrate that strong TCSn activation still occurs and that this response is greatly diminished in cytokinin receptor mutants. Although intracellular receptors play significant roles, we argue for a revision of concepts of cytokinin perception to include the spatial dimensions. In particular, selective ligand-receptor affinities, cellular localisation and tissue distribution of bioactive cytokinins, their receptors, transporters and inactivation enzymes appear all to be components of the signalling regulatory mechanisms.

plant biology↗

bioRxiv2019

Anaesthesia with diethyl ether impairs jasmonate signalling in the carnivorous plant Venus flytrap (Dionaea muscipula).

General anaesthetics are compounds that induce loss of responsiveness to environmental stimuli in animals and humans. The primary site of general anaesthetic action is the nervous system, where anaesthetics inhibit neuronal transmission. Although plants do not have neurons, they generate electrical signals in response to biotic and abiotic stresses. Here, we investigated the effect of the general volatile anaesthetic diethyl ether on the ability to sense potential prey or herbivore attacks in the carnivorous plant Venus flytrap (Dionaea muscipula). We monitored trap movement, electrical signalling, phytohormone accumulation and gene expression in response to the mechanical stimulation of trigger hairs and wounding under diethyl ether treatment. Diethyl ether completely inhibited the generation of action potentials and trap closing reactions, which were easily and rapidly restored when the anaesthetic was removed. Diethyl ether also inhibited the later response: jasmonate (JA) accumulation and expression of JA-responsive genes. However, external application of JA bypassed the inhibited action potentials and restored gene expression under diethyl ether anaesthesia, indicating that downstream reactions from JA are not inhibited. Thus, the Venus flytrap cannot sense prey or a herbivore attack under diethyl ether treatment. This is an intriguing parallel to the effect of anaesthesia on animals and humans.\n\nHighlightCarnivorous plant Venus flytrap (Dionaea muscipula) is unresponsive to insect prey or herbivore attack due to impaired electrical and jasmonate signalling under general anaesthesia induced by diethyl ether.

plant biology↗

bioRxiv2019

Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots

Directional organ growth allows the plant root system to strategically cover its surroundings. Intercellular auxin transport is aligned with the gravity vector in the primary root tips, facilitating downward organ bending at the lower root flank. Here we show that cytokinin signaling functions as a lateral root specific anti-gravitropic component, promoting the radial distribution of the root system. We performed a genome-wide association study and revealed that signal peptide processing of Cytokinin Oxidase 2 (CKX2) affects its enzymatic activity and, thereby, determines the degradation of cytokinins in natural Arabidopsis thaliana accessions. Cytokinin signaling interferes with growth at the upper lateral root flank and thereby prevents downward bending. Our interdisciplinary approach revealed that two phytohormonal cues at opposite organ flanks counterbalance each others negative impact on growth, suppressing organ growth towards gravity and allow for radial expansion of the root system.

plant biology↗

bioRxiv2019

Molecular framework for TIR1/AFB-Aux/IAA-dependent auxin sensing controlling adventitious rooting in Arabidopsis

In Arabidopsis thaliana, canonical auxin-dependent gene regulation is mediated by 23 transcription factors from the AUXIN RESPONSE FACTOR (ARF) family, most of which interact with 29 auxin/indole acetic acid (Aux/IAA) repressors, themselves forming, in the presence of auxin, coreceptor complexes with one of six TRANSPORT INHIBITOR1/AUXIN-SIGNALLING F-BOX PROTEINS (TIR1/AFB). Different combinations of co-receptors drive specific sensing outputs, allowing auxin to control a myriad of processes. Considerable efforts have been made to discern the temporal and spatial specificity of auxin action. However, owing to a lack of obvious phenotype in single loss-of-function mutants in Aux/IAA genes, most genetic studies have relied on gain-of-function mutants, which are highly pleiotropic. In this article, we describe a molecular framework for the role of several members of the auxin sensing machinery. Using loss-of-function mutants, we demonstrate that TIR1 and AFB2 are positive regulators, whereas IAA6, IAA9 and IAA17 are negative regulators of adventitious root (AR) formation. The three Aux/IAA proteins interact with ARF6 and/or ARF8, which we have previously shown to be positive regulators of AR formation upstream of jasmonate, and likely repress their activity. Our data also suggest a dual role for TIR1 in the control of JA biosynthesis and conjugation, as revealed by upregulation of several JA biosynthesis genes in the tir1-1 mutant. In conclusion, we propose that in the presence of auxin, TIR1 and AFB2 form specific sensing complexes with IAA6, IAA9 and/or IAA17 that modulate JA homeostasis to control AR initiation.\n\nSignificanceAdventitious root (AR) formation is a quantitative trait with high phenotypic plasticity and auxin plays a major role in its control. In previous studies, we have shown that, in Arabidopsis hypocotyls, AR formation is negatively regulated by jasmonate, whose homeostasis is controlled by a regulatory module composed of three AUXIN RESPONSE FACTORS (ARF), two of which are positive regulators of three auxin inducible Gretchen Hagen3 (GH3) genes. The present work demonstrates that the two F-box proteins, i.e., TIR1 and AFB2, together with at least three Aux/IAA proteins are likely to interact in a combinatorial manner to control the activity of the two activator ARFs upstream of JA biosynthesis and/or homeostasis, thereby controlling AR initiation in Arabidopsis hypocotyls.

plant biology↗

bioRxiv2018

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, Voltron, that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 minutes of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

neuroscience↗

bioRxiv2018

Anthranilic acid regulates subcellular localization of auxin transporters during root gravitropism

O_LIDistribution of auxin within plant tissues is of great importance for developmental plasticity, including root gravitropic growth. Auxin flow is directed by the subcellular polar distribution and dynamic relocalization of auxin transporters such as the PIN-FORMED (PIN) efflux carriers, which can be influenced by the main natural plant auxin indole-3-acetic acid (IAA). Anthranilic acid (AA) is an important early precursor of IAA and previously published studies with AA analogues suggested that AA may also regulate PIN localization.\nC_LIO_LIUsing Arabidopsis thaliana as a model species, we studied an AA-deficient mutant displaying agravitropic root growth, treated seedlings with AA and AA analogues and transformed lines to over-produce AA while inhibiting its conversion to downstream IAA precursors.\nC_LIO_LIWe showed that AA rescues root gravitropic growth in the AA-deficient mutant at concentrations that do not rescue IAA levels. Overproduction of AA affects root gravitropism without affecting IAA levels. Treatments with, or deficiency in, AA result in defects in PIN polarity and gravistimulus-induced PIN relocalization in root cells.\nC_LIO_LIOur results reveal a previously unknown role for AA in the regulation of PIN subcellular localization and dynamics involved in root gravitropism, which is independent of its better-known role in IAA biosynthesis.\nC_LI

plant biology↗

bioRxiv2018

Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development

Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFB functionality as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin1 to 4 (RN1 to 4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical and morphological levels. This selective activity is explained by their ability to promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, via a genetic screen using RN4, we revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions.

plant biology↗

bioRxiv2018

Kilohertz frame-rate two-photon tomography

Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits imaging speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and uses prior information to recover high-resolution images at over 1.4 billion voxels per second. Using a structural image as a prior for recording neural activity, we imaged visually-evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250 {micro}m and frame-rates over 1 kHz. Dendritic glutamate transients in anaesthetized mice are synchronized within spatially-contiguous domains spanning tens of microns at frequencies ranging from 1-100 Hz. We demonstrate high-speed recording of acetylcholine and calcium sensors, 3D single-particle tracking, and imaging in densely-labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.

neuroscience↗

bioRxiv2018

A genetically encoded fluorescent sensor for in vivo imaging of GABA

Current techniques for monitoring GABA, the primary inhibitory neurotransmitter in vertebrates, cannot follow ephemeral transients in intact neural circuits. We applied the design principles used to create iGluSnFR, a fluorescent reporter of synaptic glutamate, to develop a GABA sensor using a protein derived from a previously unsequenced Pseudomonas fluorescens strain. Structure-guided mutagenesis and library screening led to a usable iGABASnFR ({Delta}F/Fmax ~ 2.5, Kd ~ 9 M, good specificity, adequate kinetics). iGABASnFR is genetically encoded, detects single action potential-evoked GABA release events in culture, and produces readily detectable fluorescence increases in vivo in mice and zebrafish. iGABASnFR enabled tracking of: (1) mitochondrial GABA content and its modulation by an anticonvulsant; (2) swimming-evoked GABAergic transmission in zebrafish cerebellum; (3) GABA release events during inter-ictal spikes and seizures in awake mice; and (4) GABAergic tone decreases during isoflurane anesthesia. iGABASnFR will permit high spatiotemporal resolution of GABA signaling in intact preparations.

neuroscience↗

bioRxiv2018

Cellulose biosynthesis inhibition reduces cell cycle activity in a nitrate reductase- and cytokinin-dependent manner

O_LIDuring growth, development and defense, cell wall integrity needs to be coordinated with cell cycle activity. In Saccharomyces cerevisiae, coordination is mediated by the cell wall integrity maintenance mechanism. In plants, little is known how coordination is achieved.\nC_LIO_LIHere we investigated coordination between plant cell wall and cell cycle activity in Arabidopsis thaliana seedlings by studying the impact of cell wall damage (CWD, caused by cellulose biosynthesis inhibition) on cell cycle gene expression, growth, phytohormone (jasmonic acid, salicylic acid, cytokinins) and lignin accumulation.\nC_LIO_LIWe found root growth and cell cycle gene expression are reduced by CWD in an osmo-sensitive manner. trans-zeatin application suppressed the CWD effect on gene expression. Quantification of cytokinins revealed CWD-induced, osmo-sensitive changes in several cytokinins. Expression of CYTOKININ OXIDASE2/DEHYDROGENASE (CKX2) and CKX3, encoding cytokinin-degrading enzymes, was elevated in CWD-exposed seedlings. Genetic studies implicated NITRATE REDUCTASE1/2 (NIA1/2) in the response to CWD. In nia1/2 seedlings CWD induced neither expression of CKX2/3 and cell cycle genes nor accumulation of jasmonic acid, salicylic acid and lignin.\nC_LIO_LIThis suggests that CWD causes increased CKX2/3 expression through a NIA1/2-mediated process. Increased CKX expression seems to cause changes in cytokinin levels, leading to reduced cell cycle gene expression.\nC_LI

plant biology↗

bioRxiv2018

Thy1 transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging in vivo

Calcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterizarion of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by the Thy1 promoter. Four transgenic lines with different expression patterns showed sufficiently high expression for cellular in vivo imaging. We used two-photon microscopy to characterize visual responses of individual neurons in the visual cortex in vivo. The signal-to-noise ratio in transgenic mice was comparable to, or better than, for mice transduced with adeno-associated virus. We also show that Thy1-jRGECO1a transgenic mice are useful for transcranial population imaging and functional mapping using widefield fluorescecnce microscopy. We also demonstrate imaging of visual responses in retinal ganglion cells. Thy1-jRGECO1a transgenic mice are therefore a useful addition to the toolbox for imaging activity in intact neural networks.

neuroscience↗

bioRxiv2018

Root Responses to Heterogeneous Nitrate Availability are Mediated by trans-Zeatin in Arabidopsis Shoots

Plants are subjected to variable nitrogen (N) availability including frequent spatial nitrate (NO3-) heterogeneity in soil. Thus, plants constantly adapt their genome expression and root physiology in order to optimize N acquisition from this heterogeneous source. These adaptations rely on a complex and long-distance root-shoot-root signaling network that is still largely unknown. Here, we used a combination of reverse genetics, transcriptomic analysis, NO3- uptake experiments and hormone profiling under conditions of homogeneous or heterogeneous NO3- availability to characterize the systemic signaling involved. We demonstrate the important role of the trans-zeatin form of cytokinin (CK) in shoots, in particular using a mutant altered for ABCG14-mediated trans-zeatin-translocation from the root to the shoot, in mediating: (i) rapid long distance N-demand signaling and (ii) long term functional adaptations to heterogeneous NO3- supply, including changes in NO3- transport capacity and root growth modifications. We also provide insights into the potential CK-dependent and independent shoot-to-root signals involved in root adaptation to heterogeneous N availability.

plant biology↗