Zinc Excess Induces a Hypoxia-Like Response by Inhibiting Cysteine Oxidases in Poplar Roots

Thiol dioxygenases: from structures to functions

Thiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of action and the different substrate specificity of these enzymes. Concomitantly, the physiological role of thiol dioxygenation in prokaryotes and eukaryotes has been studied through genetic and physiological approaches. Further structural characterization is necessary to enable precise and safe manipulation of thiol dioxygenases (TDOs) for therapeutic, industrial, and agricultural applications.

Identification of novel plant cysteine oxidase inhibitors from a yeast chemical genetic screen

Hypoxic responses in plants involve Plant Cysteine Oxidases (PCOs). They catalyze the N-terminal cysteine oxidation of Ethylene Response Factors VII (ERF-VII) in an oxygen-dependent manner, leading to their degradation via the cysteine N-degron pathway (Cys-NDP) in normoxia. In hypoxia, PCO activity drops, leading to the stabilization of ERF-VIIs and subsequent hypoxic gene upregulation. Thus far, no chemicals have been described to specifically inhibit PCO enzymes. In this work, we devised an in vivo pipeline to discover Cys-NDP effector molecules. Budding yeast expressing AtPCO4 and plant-based ERF-VII reporters was deployed to screen a library of natural-like chemical scaffolds and was further combined with an Arabidopsis Cys-NDP reporter line. This strategy allowed us to identify three PCO inhibitors, two of which were shown to affect PCO activity in vitro. Application of these molecules to Arabidopsis seedlings led to an increase in ERF-VII stability, induction of anaerobic gene expression, and improvement of tolerance to anoxia. By combining a high-throughput heterologous platform and the plant model Arabidopsis, our synthetic pipeline provides a versatile system to study how the Cys-NDP is modulated. Its first application here led to the discovery of at least two hypoxia-mimicking molecules with the potential to impact plant tolerance to low oxygen stress.

ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana

Oxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PLANT CYSTEINE OXIDASE (PCO) N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain untested or unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance and are essential for root development and survival under oxygen limiting conditions in soil. We determine the combined effects of ERFVIIs in controlling gene expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.

Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes

N-terminal cysteine oxidases (NCOs) use molecular oxygen to oxidise the amino-terminal cysteine of specific proteins, thereby initiating the proteolytic N-degron pathway. To expand the characterisation of the plant family of NCOs (plant cysteine oxidases [PCOs]), we performed a phylogenetic analysis across different taxa in terms of sequence similarity and transcriptional regulation. Based on this survey, we propose a distinction of PCOs into two main groups. A-type PCOs are conserved across all plant species and are generally unaffected at the messenger RNA level by oxygen availability. Instead, B-type PCOs appeared in spermatophytes to acquire transcriptional regulation in response to hypoxia. The inactivation of two A-type PCOs in Arabidopsis thaliana, PCO4 and PCO5, is sufficient to activate the anaerobic response in young seedlings, whereas the additional removal of B-type PCOs leads to a stronger induction of anaerobic genes and impairs plant growth and development. Our results show that both PCO types are required to regulate the anaerobic response in angiosperms. Therefore, while it is possible to distinguish two clades within the PCO family, we conclude that they all contribute to restrain the anaerobic transcriptional programme in normoxic conditions and together generate a molecular switch to toggle the hypoxic response.

ERF subfamily transcription factors and their function in plant responses to abiotic stresses

Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K⁺ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.

In Vivo Imaging of Plant Oxygen Levels

Oxygen is essential for multicellular aerobic life due to its central role in energy metabolism. The availability of oxygen can drop below the level to sustain oxidative phosphorylation when plants are flooded, posing a severe threat to survival. However, under non-stressful conditions, the internal oxygen concentration of most plant tissue is not in equilibrium with the environment, which is attributed to cellular respiration and diffusion constrains imposed by O2 barriers and bulky tissue. This is exemplified by the observations of steep oxygen gradients in roots, fruits, tubers, anthers and meristems. To adapt to a varying availability of oxygen, plants sense O2 via the conditional proteolysis of transcriptional regulators. This mechanism acts to switch oxidative metabolism to anaerobic fermentation, but it was also shown to play a role in plant development and pathogen defense. To investigate how dynamic and spatial distribution of O2 impacts on these processes, accurate mapping of its concentration in plants is essential. Physical oxygen sensors have been employed for decades to profile internal oxygen concentrations in plants, while genetically encoded oxygen biosensors have only recently started to see use. Driven by the critical role of hypoxia in human pathology and development, several novel oxygen-sensing devices have also been characterized in cell lines and animal model organisms. This review aims to provide an overview of available oxygen biosensors and to discuss their potential application to image oxygen levels in plants.

The multifactorial assessment of the Zn impact on high and low temperature stress towards wheat seedling growth under diverse moisture conditions (optimal and wet) in three soils

Anthropogenic activities leading to chemical contamination of soil and global climate change may increase the level of stress for plants. Recent decades studies (mainly two-factors) have reported that the ecotoxicity of soil contaminants could be modified by climate factors. To date, little is known about: the combined climate-chemical stress on plants; the interaction of chemicals with high soil moisture conditions; the impact of soil properties on the combined climate-chemical stress and questions regarding the response of organisms to combined effect of all key factors influencing the ecotoxicity of chemicals under field conditions remain unanswered. Our study sought to fill the knowledge gap on the multifactorial interaction of four main factors encounter in polluted areas (soil chemical contamination: heavy metal (Zn); temperature: 10, 23, 35 °C, moisture: 55, 80%WHC; soil properties). The assessment of combined effect of multiple stressors based on the multiple ANCOVA model (n = 108; adjusted R² = 0.68) and calculated indicators showed: 1) all studied factors significantly interacted and influenced the phytotoxic effect of Zn; 2) Zn modified the plant response to temperature stress depending on moisture conditions and soil properties. This study improves methods for assessing the hazardous effects of soil chemical contamination in the real environment.

Comparative Biology of Oxygen Sensing in Plants and Animals

Aerobic respiration is essential to almost all eukaryotes and sensing oxygen is a key determinant of survival. Analogous but mechanistically different oxygen-sensing pathways were adopted in plants and metazoan animals, and include ubiquitin-mediated degradation of transcription factors and direct sensing via non-heme iron(Fe²⁺)-dependent-dioxygenases. Key roles for oxygen sensing have been identified in both groups, with downstream signalling focussed on regulating gene transcription and chromatin modification to control development and stress responses. Components of sensing systems are promising targets for human therapeutic intervention and developing stress-resilient crops. Here, we review current knowledge about the origins, commonalities and differences between oxygen sensing in plants and animals.

Zinc toxicity in plants: a review

This review highlights the most recent updated information available about Zn phytotoxicity at physiological, biochemical and molecular levels, uptake mechanisms as well as excess Zn homeostasis in plants. Zinc (Zn) is a natural component of soil in terrestrial environments and is a vital element for plant growth, as it performs imperative functions in numerous metabolic pathways. However, potentially noxious levels of Zn in soils can result in various alterations in plants like reduced growth, photosynthetic and respiratory rate, imbalanced mineral nutrition and enhanced generation of reactive oxygen species. Zn enters into soils through various sources, such as weathering of rocks, forest fires, volcanoes, mining and smelting activities, manure, sewage sludge and phosphatic fertilizers. The rising alarm in environmental facet, as well as, the narrow gap between Zn essentiality and toxicity in plants has drawn the attention of the scientific community to its effects on plants and crucial role in agricultural sustainability. Hence, this review focuses on the most recent updates about various physiological and biochemical functions perturbed by high levels of Zn, its mechanisms of uptake and transport as well as molecular aspects of surplus Zn homeostasis in plants. Moreover, this review attempts to understand the mechanisms of Zn toxicity in plants and to present novel perspectives intended to drive future investigations on the topic. The findings will further throw light on various mechanisms adopted by plants to cope with Zn stress which will be of great significance to breeders for enhancing tolerance to Zn contamination.

The Geomagnetic Field Is a Contributing Factor for an Efficient Iron Uptake in Arabidopsis thaliana

The Earth's magnetic field, defined as the geomagnetic field (GMF), is an unavoidable environmental factor for all living organisms. Variation in the GMF intensity was found to affect the content of some nutrients and their associated channels and transporters in Arabidopsis thaliana. In this work, we observed that reduction of the GMF to near null magnetic field (NNMF) affects the accumulation of metals in plant tissues, mainly iron (Fe) and zinc (Zn) content, while the content of others metals such as copper (Cu) and manganese (Mn) is not affected. Accordingly, Fe uptake genes were induced in the roots of NNMF-exposed plants and the root Fe reductase activity was affected by transferring GMF-exposed plant to NNMF condition. Under Fe deficiency, NNMF-exposed plants displayed a limitation in the activation of Fe-deficiency induced genes. Such an effect was associated with the strong accumulation of Zn and Cu observed under NNMF conditions. Overall, our results provide evidence on the important role of the GMF on the iron uptake efficiency of plants.

The Contribution of Plant Dioxygenases to Hypoxia Signaling

Dioxygenases catalyze the incorporation of one or two oxygen atoms into target organic substrates. Besides their metabolic role, these enzymes are involved in plant signaling pathways as this reaction is in several instances required for hormone metabolism, to control proteostasis and regulate chromatin accessibility. For these reasons, alteration of dioxygenase expression or activity can affect plant growth, development, and adaptation to abiotic and biotic stresses. Moreover, the requirement of co-substrates and co-factors, such as oxygen, 2-oxoglutarate, and iron (Fe²⁺), invests dioxygenases with a potential role as cellular sensors for these molecules. For example, inhibition of cysteine deoxygenation under hypoxia elicits adaptive responses to cope with oxygen shortage. However, biochemical and molecular evidence regarding the role of other dioxygenases under low oxygen stresses is still limited, and thus further investigation is needed to identify additional sensing roles for oxygen or other co-substrates and co-factors. Here, we summarize the main signaling roles of dioxygenases in plants and discuss how they control plant growth, development and metabolism, with a focus on the adaptive responses to low oxygen conditions.

The plant N-degron pathways of ubiquitin-mediated proteolysis

The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.

The Geomagnetic Field Is a Contributing Factor for an Efficient Iron Uptake in Arabidopsis thaliana

The Earth's magnetic field, defined as the geomagnetic field (GMF), is an unavoidable environmental factor for all living organisms. Variation in the GMF intensity was found to affect the content of some nutrients and their associated channels and transporters in Arabidopsis thaliana. In this work, we observed that reduction of the GMF to near null magnetic field (NNMF) affects the accumulation of metals in plant tissues, mainly iron (Fe) and zinc (Zn) content, while the content of others metals such as copper (Cu) and manganese (Mn) is not affected. Accordingly, Fe uptake genes were induced in the roots of NNMF-exposed plants and the root Fe reductase activity was affected by transferring GMF-exposed plant to NNMF condition. Under Fe deficiency, NNMF-exposed plants displayed a limitation in the activation of Fe-deficiency induced genes. Such an effect was associated with the strong accumulation of Zn and Cu observed under NNMF conditions. Overall, our results provide evidence on the important role of the GMF on the iron uptake efficiency of plants.

A Ratiometric Sensor Based on Plant N-Terminal Degrons Able to Report Oxygen Dynamics in Saccharomyces cerevisiae

The ability to perceive oxygen levels is crucial to many organisms because it allows discerning environments compatible with aerobic or anaerobic metabolism, as well as enabling rapid switch between these two energy strategies. Organisms from different taxa dedicate distinct mechanisms to associate oxygen fluctuations with biological responses. Following from this observation, we speculated that orthogonal oxygen sensing devices can be created by transfer of essential modules from one species to another in which they are not conserved. We expressed plant cysteine oxidase (PCOs) enzymes in Saccharomyces cerevisiae, to confer oxygen-conditional degradability to a bioluminescent protein tagged with the Cys-exposing N-degron typical of plant ERF-VII factors. Co-translation of a second luciferase protein, not subjected to oxygen-dependent proteolysis, made the resulting Double Luciferase Oxygen Reporter (DLOR) ratiometric. We show that DLOR acts as a proxy for oxygen dynamics in yeast cultures. Moreover, since DLOR activity was enabled by the PCO sensors, we employed this device to disclose some of their properties, such as the dispensability of nitric oxide for N-terminal cysteine oxidation and the individual performance of Arabidopsis PCO isoforms in vivo. In the future, we propose the synthetic DLOR device as a convenient, eukaryotic cell-based tool to easily screen substrates and inhibitors of cysteine oxidase enzymes in vivo. Replacement of the luminescent proteins with fluorescent proteins will further turn our system into a visual reporter for oxygen dynamics in living cells.