Plant Arabidopsis Thaliana Research Articles

Unravelling the different components of nonphotochemical quenching using a novel analytical pipeline.

Photoprotection in plants includes processes collectively known as nonphotochemical quenching (NPQ), which quench excess excitation-energy in photosystem II. NPQ is triggered by acidification of the thylakoid lumen, which leads to PsbS-protein protonation and violaxanthin de-epoxidase activation, resulting in zeaxanthin accumulation. Despite extensive study, questions persist about the mechanisms of NPQ. We have set up a novel analytical pipeline to disentangle NPQ induction curves measured at many light intensities into a limited number of different kinetic components. To validate the method, we applied it to Chl-fluorescence measurements, which utilised the saturating-pulse methodology, on wild-type (wt) and zeaxanthin-lacking (npq1) Arabidopsis thaliana plants. NPQ induction curves in wt and npq1 can be explained by four components ( , , and ). The fastest two ( and ) correlate with pH difference formed across the thylakoid membrane in wt and npq1. In wt, the slower component ( ) appears to be due to the formation of zeaxanthin-related quenching whilst for npq1, this component is 'replaced' by a slower component ( ), which reflects a photoinhibition-like process that appears in the absence of zeaxanthin-induced quenching. Expanding this approach will allow the effects of mutations and other abiotic-stress factors to be directly probed by changes in these underlying components.

SAGA1 and MITH1 produce matrix-traversing membranes in the CO2-fixing pyrenoid.

Approximately one-third of global CO2 assimilation is performed by the pyrenoid, a liquid-like organelle found in most algae and some plants. Specialized pyrenoid-traversing membranes are hypothesized to drive CO2 assimilation in the pyrenoid by delivering concentrated CO2, but how these membranes are made to traverse the pyrenoid matrix remains unknown. Here we show that proteins SAGA1 and MITH1 cause membranes to traverse the pyrenoid matrix in the model alga Chlamydomonas reinhardtii. Mutants deficient in SAGA1 or MITH1 lack matrix-traversing membranes and exhibit growth defects under CO2-limiting conditions. Expression of SAGA1 and MITH1 together in a heterologous system, the model plant Arabidopsis thaliana, produces matrix-traversing membranes. Both proteins localize to matrix-traversing membranes. SAGA1 binds to the major matrix component, Rubisco, and is necessary to initiate matrix-traversing membranes. MITH1 binds to SAGA1 and is necessary for extension of membranes through the matrix. Our data suggest that SAGA1 and MITH1 cause membranes to traverse the matrix by creating an adhesive interaction between the membrane and matrix. Our study identifies and characterizes key factors in the biogenesis of pyrenoid matrix-traversing membranes, demonstrates the importance of these membranes to pyrenoid function and marks a key milestone toward pyrenoid engineering into crops for improving yields.

Carbon and nitrogen signaling regulate FLOWERING LOCUS C and impact flowering time in Arabidopsis.

The timing of flowering in plants is modulated by both carbon (C) and nitrogen (N) signaling pathways. In a previous study, we established a pivotal role of the sucrose-signaling trehalose 6-phosphate pathway in regulating flowering under N-limited short-day conditions. In this work, we show that both wild-type Arabidopsis (Arabidopsis thaliana) plants grown under N-limited conditions and knock-down plants of TREHALOSE PHOSPHATE SYNTHASE 1 induce FLOWERING LOCUS C (FLC) expression, a well-known floral repressor associated with vernalization. When exposed to an extended period of cold, a flc mutant fails to respond to N availability and flowers at the same time under N-limited and full-nutrition conditions. Our data suggest that SUCROSE NON-FERMENTING 1 RELATED KINASE 1-dependent trehalose 6-phosphate-mediated C signaling and a mechanism downstream of N signaling (likely involving NIN-LIKE PROTEIN 7) impact the expression of FLC. Collectively, our data underscore the existence of a multi-factor regulatory system in which the C and N signaling pathways jointly govern the regulation of flowering in plants.

Interspecific competition reduces seed dispersal in an annual plant and slows simulated range expansions

Understanding the factors influencing how fast populations can spread across the landscape will be crucial as species ranges shift due to climate change. While the role of abiotic factors in determining expansion speed has been well studied in theory and empirical research, how competition impacts speed has received far less attention. Here, we investigated how seed dispersal distances change in response to competition and how these changes to distributions of dispersed seeds impact expansion speed. We dispersed four genotypes of the annual plant Arabidopsis thaliana with variation in life history traits into greenhouse mesocosms of either empty habitat or habitat containing the annual grass competitor, Lolium multiflorum. We found that competition decreased both mean and maximum dispersal distance. We then built a simulation model of range expansion with experimental data from this and a prior experiment to explore whether competition slows species expansions primarily through decreasing dispersal or fecundity. We found that competition primarily slows expansion speed through decreases in dispersal, but that when competition impacts both dispersal and fecundity, expansions slow more than with dispersal alone. The genotype with traits associated with longer distance dispersal was the most affected by competition in both experimental dispersal and simulations. This research suggests that not only does competition slow range expansions through decreases in both fecundity and dispersal, but that there may be consequences for evolutionary processes at the leading edge.

Analysis of abiotic and biotic stress-induced Ca2+ transients in the crop species Solanum tuberosum.

Secondary messengers, such as calcium ions (Ca2+), are integral parts of a system that transduces environmental stimuli into appropriate cellular responses. Different abiotic and biotic stresses as well as developmental processes trigger temporal increases in cytosolic free Ca2+ levels by an influx from external and internal stores. Stimulus-specificity is obtained by a certain amplitude, duration, oscillation and localisation of the response. Most knowledge on stress-specific Ca2+ transient, called calcium signatures, has been gained in the model plant Arabidopsis thaliana, while reports about stress-related Ca2+ signalling in crop plants are comparatively scarce. In this study, we introduced the Ca2+ biosensor apoaequorin into potato (Solanum tuberosum, Lcv.Désirée). We observed dose-dependent calcium signatures in response to a series of stress stimuli, including H2O2, NaCl, mannitol and pathogen-associated molecular patterns (PAMPs) with stimuli-specific kinetics. Direct comparison with Arabidopsis revealed differences in the kinetics and amplitude of Ca2+ transients between both species, implying species-specific sensitivity for different stress conditions. The potato line generated in this work provides a useful tool for further investigations on stress-induced signalling pathways, which could contribute to the generation of novel, stress-tolerant potato varieties.

Structure-aware annotation of leucine-rich repeat domains.

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.

Evaluation and identification of metabolites produced by Cytobacillus firmus in the interaction with Arabidopsis thaliana plants and their effect on Solanum lycopersicum

Evaluation and identification of metabolites produced by Cytobacillus firmus in the interaction with Arabidopsis thaliana plants and their effect on Solanum lycopersicum

Metarhizium fight club: Within-host competitive exclusion and resource partitioning.

Both Metarhizium robertsii ARSEF 2575 (Mr2575) and Metarhizium anisopliae ARSEF 549 (Ma549) infect a range of insects whilst also interacting with plants; however, little is known about the traits that affect the competitive ability of different strains. We examined the interactions between Mr2575 and Ma549 in culture and during co-infection of plants (Arabidopsis thaliana) and insects. Mr2575 outcompetes Ma549 under nutrient-limiting conditions, including root exudates, giving it a priority advantage on Arabidopsis roots. However, during co-infection of Manduca sexta or Drosophila melanogaster, Ma549's higher blastospore production enhanced its competitive ability within the host. In large M. sexta (fifth instar), blastospores facilitate dispersal, suppress host melanization and prevent Mr2575 from spreading from infection sites, reducing conidia production. However, colonization of smaller hosts such as first instar M. sexta and D. melanogaster did not provide Ma549 with a competitive advantage, as conidial production was dependent on retaining control of the cuticle through which conidiating hyphae emerge. Unexpectedly, Ma549 and Mr2575 segregate within hosts, suggesting resource partitioning with Mr2575 predominating in the thoraxes of Drosophila, especially in females, and Ma549 in the abdomen. In fifth instar M. sexta, Mr2575 was most prevalent around spiracles and the front end of segments, despite Ma549 and Mr2575 having similar susceptibility to hypoxia. Dispersing conidia homogeneously into the hemocoel of fifth instar M. sexta eliminated the blastospore production advantage, making Ma549 and Mr2575 equally competitive, with strict partitioning of Mr2575 at the anterior and Ma549 at the posterior ends of segments. As Metarhizium species have multiple roles in natural ecosystems and agroecosystems these discoveries are relevant to understanding their impact on maintaining biodiversity and for exploiting them to enhance food security.

WOX1 controls leaf serration development via temporally restricting BZR1 and CUC3 expression in Arabidopsis.

Leaves evolve shape diversity ranging from simple leaves with smooth margin to complicated shape with toothed/serrated, lobed and dissected leaves with leaflets. In the model plant Arabidopsis thaliana with simple leaves producing serrated margin, boundary regulatory factors CUP SHAPED COTYLEDON 2 (CUC2) and CUC3 play important roles in promoting leaf serration initiation and maintenance. Stem cell related WUSCHEL-RELATED HOMEOBOX1 (WOX1) and PRESSED FLOWER/WOX3 are also essential for leaf margin morphogenesis, but the role of WOX1 and PRS as well as the relationships between CUCs and WOXs on tooth development was unclear. In this study, we found that WOX1, but not PRS, prevents overproduction of tooth number and excessive tooth size by limiting CUC3 expression to a moderate level in a temporally regulated manner. We also revealed that BRASSINAZOLE RESISTANT 1 (BZR1), a known regulator for plant development including boundary regions, is involved in WOX1 negative regulation of tooth development by repressing CUC3 expression during the initiation/early stage of tooth development. WOX1 parallelly limits BZR1 and CUC3 expression from the late stage of the first 2 teeth, while restricts CUC3 activity in a BZR1 dependent manner from the initiation/early stage of subsequently developed teeth. This study uncovers a new mechanism for WOX1 in fine-tuning the leaf margin geometry.

Basic design of artificial membrane-less organelles using condensation-prone proteins in plant cells

Membrane-less organelles, formed by the condensation of biomolecules, play a pivotal role in eukaryotes. Artificial membrane-less organelles and condensates are effective tools for the creation of new cellular functions. However, it is poorly understood how to control the properties that affect condensate function, particularly in plants. Here, we report the construction of model artificial condensates using the condensation-prone proteins OsJAZ2 and AtFCA in a transient assay using rice (Oryza sativa) cells, and how condensate properties, such as subcellular localization, protein mobility, and size can be altered. We showed that proteins of interest can be recruited to condensates using nanobodies or chemically induced dimerization. Furthermore, by combining two types of condensation-prone proteins, we demonstrated that artificial hybrid condensates with heterogeneous material properties could be constructed. Finally, we showed that modified artificial condensates can be constructed in transgenic Arabidopsis thaliana plants. These results provide a framework for the basic design of synthetic membrane-less organelles in plants.

The Present State and Impact of AI-Driven Computational Tools for Predicting Plant Protein Structures.

Several key functions of plants, such as photosynthesis, nutrient transport, disease resistance, and abiotic tolerance, are manifested by several classes of proteins. Prediction of 3- dimensional (3-D) structures of proteins and their working mechanisms can have a profound impact on plant proteomics research and could help improve key agricultural traits in crop plants. This review aims to present the current status of plant protein structure determination and discuss the way forward. Most experimentally proven protein structures are available only for the model plant Arabidopsis thaliana. Most of the key crop plants have only a few hundred or fewer experimentally proven 3-D structures. Fewer than 1% of the protein sequences in the majority of plants have had their 3D structures experimentally determined, and A. thaliana is the sole plant with the highest percentage of 1.4 % of protein sequences with experimentally determined structures. AI-based protein structure prediction tool AlphaFold has predicted models of several thousand proteins for many crop plants. In AlphaFold predicted protein models, soybean has the highest percentage (65%) of its UniProt protein sequences with predicted models, and a few other crop plants have also a considerable percentage of its UniProt sequences with AlphaFold predicted models. AlphaFold might help predict models and bridge the gap in plant structure determination studies. Protein structure information might lead to engineering key residues to improve the agronomical performance of crop plants.

Choline chloride and N-allylglycine promote plant growth by increasing the efficiency of photosynthesis.

We previously reported that choline chloride and N-allylglycine stimulate photosynthesis in wheat protoplasts. Treatment of Arabidopsis thaliana and Brassica rapa plants with both compounds promoted growth and photosynthesis. To clarify the relationship between the enhancement of photosynthesis and increased growth, A. thaliana T87 cells, which show photosynthesis-dependent growth, and YG1 cells, which use sugar in the medium for growth, were treated with choline chloride or N-allylglycine. Only the T87 cells showed increased growth, suggesting that choline chloride and N-allylglycine promote growth by increasing photosynthetic activity. Transcriptome analysis using choline chloride and N-allylglycine-treated plants showed that the most abundant transcripts corresponded to photosynthetic electron transfer-related genes among the genes upregulated by both compounds. Furthermore, the compounds also upregulated genes encoding transcription factors that may control the expression of these photosynthetic genes. These results suggest that choline chloride and N-allylglycine promote photosynthesis through increased expression of photosynthetic electron transfer-related genes.

Forest tree extracts induce resistance to Pseudomonas syringae pv. tomato in Arabidopsis.

The widespread use of conventional pesticides for plant pathogen control poses significant risks to human health and the environment, and it is therefore crucial to develop environmentally friendly, human-safe alternatives to these products that offer a sustainable approach for crop protection. Here, we examined the potential of ethanolic extracts from four forest tree species for their antibacterial activity against the bacterial pathogenPseudomonas syringaepv.tomato (Pst) and their ability to trigger effective defense responses in the model plantArabidopsis thaliana. The extracts exhibited direct toxic effects against Pst and triggered the expression of defense-related genes naturally induced by oxidative stress cues or the defense elicitor salicylic acid in leaf tissue. The direct antibacterial effects of the tree extracts, together with their defense gene-inducing effectsin planta, resulted in a strong host plant-protecting effect againstPst. These findings suggest the eventual effectiveness of forest tree extracts as plant protectants against the bacterial pathogenPst. They also suggest the potential of these extracts as a sustainable, eco-friendly alternative to conventional pesticides for the management of economically important plant pathogens.

Exploring Functional Gene XsPDAT1’s Involvement in Xanthoceras sorbifolium Oil Synthesis and Its Acclimation to Cold Stress

Phospholipid: diacylglycerol acyltransferase (PDAT) is crucial in triacylglycerol (TAG) synthesis as it represents the final rate-limiting step of the acyl-CoA-independent acylation reaction. PDAT not only regulates lipid synthesis in plants, but also plays an important function in improving stress tolerance. In this study, the full-length coding sequence (CDS) of XsPDAT1, totaling 2022 base pairs and encoding 673 amino acids, was cloned from Xanthoceras sorbifolium. The relative expression of XsPDAT1 was significantly and positively correlated with oil accumulation during seed kernel development; there were some differences in the expression patterns under different abiotic stresses. Transgenic Arabidopsis thaliana plants overexpressing XsPDAT1 were obtained using the Agrobacterium-mediated method. Under low-temperature stress, the transgenic plants exhibited a smaller decrease in chlorophyll content, a smaller increase in relative conductivity, and a larger increase in POD enzyme activity and proline content in the leaves compared with the wild type. Additionally, lipid composition analysis revealed a significant increase in unsaturated fatty acids, such as oleic (C18:1) and linoleic (C18:2), in the seeds of transgenic plants compared to the wild type. These results suggest that XsPDAT1 plays a dual role in regulating the ratio of fatty acid composition and low-temperature stress in plants.

Alternative oxidase affects ascorbate metabolism in Arabidopsis thaliana plants under high-light conditions: possible links between respiratory electron transport pathways in mitochondria

Alternative oxidase affects ascorbate metabolism in Arabidopsis thaliana plants under high-light conditions: possible links between respiratory electron transport pathways in mitochondria

Transcriptomic dynamics of ABA response in Brassica napus guard cells

Drought has a significant, negative impact on crop production; and these effects are poised to increase with climate change. Plants acclimate to drought and water stress through diverse physiological responses, primarily mediated by the hormone abscisic acid (ABA). Because plants lose the majority of their water through stomatal pores on aerial surfaces of plants, stomatal closure is one of the rapid responses mediated by ABA to reduce transpirational water loss. The dynamic changes in the transcriptome of stomatal guard cells in response to ABA have been investigated in the model plant Arabidopsis thaliana. However, guard cell transcriptomes have not been analyzed in agronomically valuable crops such as a major oilseed crop, rapeseed. In this study, we investigated the dynamics of ABA-regulated transcriptomes in stomatal guard cells of Brassica napus and conducted comparison analysis with the transcriptomes of A. thaliana. We discovered changes in gene expression indicating alterations in a host of physiological processes, including stomatal movement, metabolic reprogramming, and light responses. Our results suggest the existence of both immediate and delayed responses to ABA in Brassica guard cells. Furthermore, the transcription factors and regulatory networks mediating these responses are compared to those identified in Arabidopsis. Our results imply the continuing evolution of ABA responses in Brassica since its divergence from a common ancestor, involving both protein-coding and non-coding nucleotide sequences. Together, our results will provide a basis for developing strategies for molecular manipulation of drought tolerance in crop plants.

The ascorbate peroxidase-related protein: insights into its functioning in Chlamydomonas and Arabidopsis.

We review the newly classified ascorbate peroxidase-related (APX-R) proteins, which do not use ascorbate as electron donor to scavenge H2O2. We summarize recent discoveries on the function and the characterization of the APX-R protein of the green unicellular alga Chlamydomonas reinhardtii and the land plant Arabidopsis thaliana. Additionally, we conduct in silico analyses on the conserved MxxM motif, present in most of the APX-R protein in different organisms, which is proposed to bind copper. Based on these analyses, we discuss the similarities between the APX-R and the class III peroxidases.

Olive mill wastewater as a source of defense-promoting by-products against microbial pathogens

Olive oil is a core component of the Mediterranean diet known for its nutritional properties and health benefits. Olive industry is moving to novel extraction systems for higher oil yield and quality and for waste reduction, which is a relevant problem in the process due to its toxicity and high disposal costs. Multi-Phase Decanter (DMF) is a modern two-phase system performed without adding water during the process. Using DMF, a wet by-product indicated as pâté and consisting of the fruit pulp and vegetation water (VW) is recovered. The pâté has a high content of potentially bioactive molecules that may be exploited to promote plant resistance against microbial pathogens. In this work, to identify by/products of biological interest, the VW recovered from the pâté by centrifugation was subjected to fractionation by tangential-flow membrane filtration (TFMF), combining microfiltration (MF) and ultrafiltration (UF). High-resolution NMR spectroscopy indicated the presence of bioactive molecules such as flavonoids, hydroxytyrosol and oleuropein with known antimicrobial activity. High-Performance Anion Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD) was performed to detect the presence of pectic oligosaccharides in the fractions, showing the enrichment, in the UF-concentrate fraction, of oligogalacturonides (OGs), well known for the ability to elicit defense responses and protect plants against pathogen infections. Arabidopsis thaliana plants treated with TFMF fractions displayed induction of defense responses and exhibited tolerance against microbial pathogens without adverse effects on growth and fitness. This study shows that pâté by-products can potentially be exploited in agriculture as sustainable plant phyto-protectant.

StEPF2 and StEPFL9 Play Opposing Roles in Regulating Stomatal Development and Drought Tolerance in Potato (Solanum tuberosum L.)

Stomata are essential for photosynthesis and water-use efficiency in plants. When expressed in transgenic Arabidopsis thaliana plants, the potato (Solanum tuberosum) proteins EPIDERMAL PATTERNING FACTOR 2 (StEPF2) and StEPF-LIKE9 (StEPFL9) play antagonistic roles in regulating stomatal density. Little is known, however, about how these proteins regulate stomatal development, growth, and response to water deficit in potato. Transgenic potato plants overexpressing StEPF2 (E2 plants) or StEPFL9 (ST plants) were generated, and RT-PCR and Western blot analyses were used to select two lines overexpressing each gene. E2 plants showed reduced stomatal density, whereas ST plants produced excessive stomata. Under well-watered conditions, ST plants displayed vigorous growth with improved leaf gas exchange and also showed increased biomass/yields compared with non-transgenic and E2 plants. E2 plants maintained lower H2O2 content and higher levels of stomatal conductance and photosynthetic capacity than non-transgenic and ST plants, which resulted in higher water-use efficiency and biomass/yields during water restriction. These results suggest that StEPF2 and StEPFL9 functioned in pathways regulating stomatal development. These genes are thus promising candidates for use in future breeding programs aimed at increasing potato water-use efficiency and yield under climate change scenarios.

Assessing the biochemical and genotoxic effects of low intensity 2.45GHz microwave exposure on Arabidopsis thaliana plants

ABSTRACT The electromagnetic waves of 2.45 GHz microwave frequency have become abundant in environments worldwide. This study assessed the short-term impact of low-intensity 2.45 GHz exposure on young Arabidopsis thaliana plants. The plants underwent a 48-hour exposure to continuous wave 2.45 GHz microwaves at a power density of 1.0 ± 0.1 W m−2. Experiments were conducted inside anechoic chambers. After the microwave exposure samples were subjected to morphological, genotoxicity, pigmentation, and physiochemical analysis. Microwave exposure elevated the levels of photosynthetic pigments, oxidative stress, guaiacol peroxidase activity, and ascorbic peroxidase activity in plants. Conversely, catalase activity decreased. Photosystem efficiency remained unchanged, while non-photochemical quenching increased. Leaf morphological parameters exhibited no significant alterations during this brief exposure period. Notably, despite shifts in physiological parameters and pigmentations, genomic template stability remained unaffected. The findings suggest that the non-thermal effects of microwave exposure influence the photosystem and plant physiology. Research confirmed the existence of non-thermal effects of microwave exposure; however, these effects are within tolerable limits for Arabidopsis thaliana plants.