Biology subjects

Giuntoli, B.

Publications and source records attributed to Giuntoli, B..

9 recordsLinked to original sources

bioRxiv2025

KDM7-mediated oxygen sensing reprograms chromatin to enhance hypoxia tolerance in the root

Roots frequently encounter low oxygen (hypoxia) from soil compaction or water saturation and must adapt to this stress. We investigated how root tip cells sense hypoxia and adjust the meristem epigenome to activate genes that promote tolerance and growth under oxygen limitation. In Arabidopsis root tips, hypoxia tolerance was linked to increased trimethylation of histone H3 at lysine 4 (H3K4me3). We also found that group 7 demethylases (KDM7s) are directly inhibited by hypoxia, and that genetic inactivation of KDM7s, like hypoxia, induces expression of genes essential for meristem survival under oxygen deprivation. We propose that KDM7s function as root-specific oxygen sensors that prime and support hypoxia tolerance.

plant biology↗

bioRxiv2025

Hydrogen sulfide modulates plant hypoxic responses through the persulfidation of Plant Cysteine Oxidases

Hydrogen sulfide (H2S) is a gaseous molecule historically regarded as toxic. Nevertheless, increasing evidence has brought to light important physiological roles in both animals and plants. In plants, H2S is involved in environmental and developmental responses, such as stomatal closure and seed germination, and in tolerance mechanisms to different stress conditions like salinity, drought and waterlogging. In this study, we report a function of H2S as a modulator of hypoxic responses in Arabidopsis thaliana. A combination of biochemical and genetic evidence demonstrates that H2S inhibits the activity of Plant Cysteine Oxidases, the molecular sensors of oxygen, through protein persulfidation to modulate hypoxia-associated responses. Furthermore, we show that H2S physiology contributes to responses to low oxygen, as disturbing H2S production impaired activation of hypoxia-responsive genes and submergence tolerance. Overall, this work introduces H2S as signalling modulator in plant hypoxic responses and adds a regulatory layer to the plant oxygen-sensing mechanism.

plant biology↗

bioRxiv2025

A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants

Plants face hypoxic conditions either chronically, as particular tissues are characterized by fluctuating or stable low oxygen levels, or acutely, when flooded. In vascular plants, transcriptional adaptive responses to hypoxia are rapidly mounted by Ethylene Response Factors VII (ERFVIIs), regulated by Plant Cysteine Oxidases (PCOs) through the cysteine branch of the N-degron pathway (Cys-NDP) for oxygen sensing. However, this relatively simple regulatory circuit, consisting of both constitutively expressed as well as hypoxia-inducible ERFVIIs and PCOs, interacts with diverse signalling cues and pathways invoked by hypoxia. To understand the share of the PCO-mediated oxygen sensing mechanism in the production of hypoxia responses, we insulated the PCO/ERFVII circuit from Arabidopsis thaliana and adapted it to Saccharomyces cerevisiae. Using a reporter gene to monitor the output of the circuit allowed us to compare the speed and amplitude of response to hypoxia in the engineered yeast and the source organism. Hypoxia triggered ERFVII stabilization both in Arabidopsis and yeast, leading to a similarly fast transcriptional response that was however larger in plants. A simple hypoxia-inducible feedback loop improved the amplitude of response in yeast, demonstrating the importance of this regulation in the endogenous PCO/ERFVII circuit. Finally, computational modelling of the yeast circuit enabled us to identify promoter competition and presence of hypoxia-inducible PCOs as key parameters that shape early hypoxia responses in plant cells. Significance StatementWe report the design, testing and optimisation of a synthetic molecular switch that activates gene expression in response to hypoxia in the yeast Saccharomyces cerevisiae. This is based on enzymes that consume molecular oxygen to regulate the stability of transcription factors in plant cells. By generating such a hybrid molecular device, we were able to demonstrate the efficacy of this hypoxia response strategy independently of the many ancillary components that affect gene regulation in plant cells. In this way, we were able to assess its activation dynamics, characterised by similarly fast induction of gene expression in both yeast and plants. Our approach also revealed the requirement of interlocked feedback loops to achieve the magnitude of gene induction measured in plants.

plant biology↗

bioRxiv2025

Severe Fe deficiency promotes hypoxia inducible responses in Arabidopsis thaliana

In plants, Fe homeostasis and O2 metabolism are strictly related, indeed several Fe-requiring enzymes catalyze reactions that also involve oxygen, as a reagent, product, entry or end point of the metabolic pathway in which the enzyme takes part. Oxygen sensing itself relies on Fe-dependent enzymes, the Plant cysteine oxidase (PCO) family of 2-OG independent thiol dioxygenases. PCOs are responsible for the degradation of ERFVII ethylene-responsive factors through a proteasomal N-degron pathway that connects hypoxia-inducible responses to the stabilization of the ERFVII transcription factors. Here, we investigated the interplay between low oxygen and Fe-deficiency stresses in A. thaliana. We used plants expressing a genetically encoded reporter of ERFVII protein stability and measured the expression of anaerobic genes to infer PCO activity in vivo. Our results highlight that Fe deprivation can elicit hypoxia-like responses depending on its severity. To test the involvement the ERFVII factors further, we examined the response of a pentuple erfVII mutant to Fe-deficiency stress, individually or combined with low oxygen. Our data indicate that the ERFVIIs might take part to the acclimation to chronic Fe deficiency by acting as positive regulators of starvation-responsive genes. Moreover, our results suggest that the ERFVIIs fine-tune nutrient mobilization to the shoots of submerged plants growing on moderately Fe-deficient substrates. This work expands the known functions of the ERFVII factors and provides new information to understand plant responses to combined environmental stresses.

plant biology↗

bioRxiv2024

Engineering prolyl hydroxylase-dependent proteolysis enables the orthogonal control of hypoxia responses in plants

Vascular plants and metazoans use selective proteolysis of transcription factors to control the adaptive responses to hypoxia, although through distinct biochemical mechanisms. The reason for this divergence is puzzling, especially when considering that the molecular components necessary to establish both strategies are conserved across the two kingdoms. To explore an alternative evolutionary scenario where plants sense hypoxia as animals do, we engineered a three-components system aimed to target proteins for degradation in an oxygen dependent manner in Arabidopsis thaliana. Applying the synthetic biology framework, we produced a hypoxia-responsive switch independent of endogenous pathways. When applied to control transcription, the synthetic system partially restored hypoxia responsiveness in oxygen-insensitive mutants. Additionally, we demonstrated its potential to regulate growth under flood-induced hypoxia. Our work highlights the use of synthetic biology to reprogram signalling pathways in plants, providing insights into the evolution of oxygen sensing and ofering tools for crop improvement under stress conditions.

synthetic biology↗

bioRxiv2024

H2O2 repurposes the plant oxygen-sensing machinery to control the transcriptional response to oxidative stress

Plants sense reduced oxygen availability (hypoxia) through Plant Cysteine Oxidases (PCOs). Reduced PCO activity in hypoxia, as seen during submergence, stabilises Group VII Ethylene Response Factors (ERFVIIs), master regulators of adaptive metabolic and anatomic responses. Equally important is timely arrest of these responses upon reoxygenation, assumed to occur through ERFVII degradation. Reoxygenation involves reactive oxygen species (ROS) production. Here, we report that instead of degradation, reoxygenation results in ERFVII nuclear stabilisation, an effect mimicked by direct H2O2 treatment. Interestingly, typical hypoxia marker genes are repressed while genes involved in ROS homeostasis and oxidative stress protection are upregulated. Using in planta, heterologous and biochemical assays, we reveal that ROS-related ERFVII stabilisation is caused by PCO inactivation. Stabilised ERFVIIs are retained at hypoxia-responsive promoters but become repressors. Our findings suggest that by responding to both oxygen and ROS, PCOs coordinate ERFVII stability to regulate timely responses to damaging fluctuations in oxygen availability.

plant biology↗

bioRxiv2021

A synthetic switch based on orange carotenoid protein to control blue light responses in chloroplasts

ABSTRACTSynthetic biology approaches to engineer light-responsive system are widely used, but their applications in plants are still limited, due to the interference with endogenous photoreceptors. Cyanobacteria, such as Synechocystis spp., possess a soluble carotenoid associated protein named Orange Carotenoid binding Protein (OCP) that, when activated by blue-green light, undergoes reversible conformational changes that enable photoprotection of the phycobilisomes. Exploiting this system, we developed a new chloroplast-localized synthetic photoswitch based on a photoreceptor-associated protein-fragment complementation assay (PCA). Since Arabidopsis thaliana does not possess the prosthetic group needed for the assembly of the OCP2 protein, we implemented the carotenoid biosynthetic pathway with a bacterial {beta}-carotene ketolase enzyme (crtW), to generate keto-carotenoids producing plants. The novel photoswitch was tested and characterized in Arabidopsis protoplasts with experiments aimed to uncover its regulation by light intensity, wavelength, and its conversion dynamics. We believe that this pioneer study establishes the basis for future implementation of plastid optogenetics to regulate organelle responses, such as gene transcription or enzymatic activity, upon exposure to specific light spectra. One-sentence summaryInspired by the light-driven conformational transitions of orange carotenoid proteins of cyanobacteria, we generated a molecular device able to switch its dimeric state in response to blue light.

synthetic biology↗

bioRxiv2020

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

N-terminal cysteine oxidases (NCOs) are enzymes that use molecular oxygen to oxidize the amino-terminal cysteine of specific proteins, thereby initiating the proteolytic N-degron pathway and thus conferring them oxygen-dependent instability. To expand the characterization of the plant family of NCOs (PCOs), we performed a phylogenetic analysis across different plant 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 and B-type sequences. A-type PCOs are conserved across all plant species and are generally unaffected at the mRNA level by oxygen availability. Instead, B-type PCOs differentiated in spermatophytes to acquire specific amino acid features and transcriptional regulation in response to hypoxia. Both groups of PCO proteins possess the ability to destabilize Cys-initiating proteins. Indeed, the inactivation of two A-type PCOs in Arabidopsis thaliana, PCO4 and PCO5, is sufficient to activate, at least partially, 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 angiosperm. Therefore, while it is possible to distinguish two clades within the PCO family, separated by both amino acid features and transcriptional regulation, we conclude that they both contribute to restrain the anaerobic transcriptional program in normoxic conditions and together generate a molecular switch to toggle the hypoxic response in Arabidopsis.One sentence summary Hypoxic induction of Plant Cysteine Oxidases has been acquired and fixed in seed plants by ancestor proteins able to initiate the proteolysis of Cys-initiating protein substrates by the Arg/N-degron pathway.View Full Text

plant biology↗

bioRxiv2020

Differential submergence tolerance between juvenile and adult Arabidopsis plants involves the ANAC017 transcription factor

Plants need to attune stress responses to the ongoing developmental programs to maximize their efficacy. For instance, successful submergence adaptation is often associated to a delicate poise between saving resources and their expenditure to activate measures that allow stress avoidance or attenuation. We observed a significant decrease in submergence tolerance associated with aging in Arabidopsis thaliana, with a critical step between two and three weeks of post-germination development. This sensitization to flooding was concomitant with the transition from juvenility to adulthood. Transcriptomic analyses indicated that a group of genes related to ABA and oxidative stress response was more expressed in juvenile plants than in adult ones. These genes are induced by endomembrane tethered ANAC factors that were in turn activated by submergence-associated oxidative stress. A combination of molecular, biochemical and genetic analyses showed that these genes are located in genomic regions that move towards a heterochromatic state with adulthood, as marked by lysine 4 dimethylation of histone H3. We concluded that, while the mechanism of flooding stress perception and signal transduction were unaltered between juvenile and adult phases, the sensitivity that these mechanisms set into action is integrated, via epigenetic regulation, into the developmental programme of the plant.

plant biology↗