Emerging roles of protein phosphorylation in plant iron homeostasis

IMA peptides are dwarf giants fighting for fitness

IRON MAN (IMA) peptides have a critical role in iron uptake and homeostasis, but whether and how they associate with plant immunity signaling remain unclear. Recently, Cao et al. provided intriguing insights into the underlying plant mechanisms that restrict root iron acquisition on perception of microorganism-associated molecular patterns (MAMPs) by spatial IMA-1 turnover.

Reducing Heavy Metal Contamination in Soil and Water Using Phytoremediation

The increase in industrialization has led to an exponential increase in heavy metal (HM) soil contamination, which poses a serious threat to public health and ecosystem stability. This review emphasizes the urgent need to develop innovative technologies for the environmental remediation of intensive anthropogenic pollution. Phytoremediation is a sustainable and cost-effective approach for the detoxification of contaminated soils using various plant species. This review discusses in detail the basic principles of phytoremediation and emphasizes its ecological advantages over other methods for cleaning contaminated areas and its technical viability. Much attention has been given to the selection of hyperaccumulator plants for phytoremediation that can grow on heavy metal-contaminated soils, and the biochemical mechanisms that allow these plants to isolate, detoxify, and accumulate heavy metals are discussed in detail. The novelty of our study lies in reviewing the mechanisms of plant-microorganism interactions that greatly enhance the efficiency of phytoremediation as well as in discussing genetic modifications that could revolutionize the cleanup of contaminated soils. Moreover, this manuscript discusses potential applications of phytoremediation beyond soil detoxification, including its role in bioenergy production and biodiversity restoration in degraded habitats. This review concludes by listing the serious problems that result from anthropogenic environmental pollution that future generations still need to overcome and suggests promising research directions in which the integration of nano- and biotechnology will play an important role in enhancing the effectiveness of phytoremediation. These contributions are critical for environmental scientists, policy makers, and practitioners seeking to utilize phytoremediation to maintain the ecological stability of the environment and its restoration.

Ethylene signaling modulates air humidity responses in plants

Air humidity significantly impacts plant physiology. However, the upstream elements that mediate humidity sensing and adaptive responses in plants remain largely unexplored. In this study, we define high humidity-induced cellular features of Arabidopsis plants and take a quantitative phosphoproteomics approach to obtain a high humidity-responsive landscape of membrane proteins, which we reason are likely the early checkpoints of humidity signaling. We found that a brief high humidity exposure (i.e., 0.5 h) is sufficient to trigger extensive changes in membrane protein abundance and phosphorylation. Enrichment analysis of differentially regulated proteins reveals high humidity-sensitive processes such as 'transmembrane transport', 'response to abscisic acid', and 'stomatal movement'. We further performed a targeted screen of mutants, in which high humidity-responsive pathways/proteins are disabled, to uncover genes mediating high humidity sensitivity. Interestingly, ethylene pathway mutants (i.e., ein2 and ein3eil1) display a range of altered responses, including hyponasty, reactive oxygen species level, and responsive gene expression, to high humidity. Furthermore, we observed a rapid induction of ethylene biosynthesis genes and ethylene evolution after high humidity treatment. Our study sheds light on the potential early signaling events in humidity perception, a fundamental but understudied question in plant biology, and reveals ethylene as a key modulator of high humidity responses in plants.

Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae

Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.

Molecular hydrogen positively regulates nitrate uptake and seed size by targeting nitrate reductase

Although the sources of molecular hydrogen (H2) synthesis in plants remain to be fully elucidated, ample evidence shows that plant-based H2 can regulate development and stress responses. Here, we present genetic and molecular evidence indicating that nitrate reductase (NR) might be a target of H2 sensing that positively regulates nitrogen use efficiency (NUE) and seed size in Arabidopsis (Arabidopsis thaliana). The expression level of NR and changes of NUE under control and, in particular, low nitrogen supply were positively associated with H2 addition supplied exogenously or through genetic manipulation. The improvement in nitrate assimilation achieved by H2 was also mediated via NR dephosphorylation. H2 control of seed size was impaired by NR mutation. Further genetic evidence revealed that H2, NR, and nitric oxide can synergistically regulate nitrate assimilation in response to N starvation conditions. Collectively, our data indicate that NR might be a target for H2 sensing, ultimately positively regulating nitrate uptake and seed size. These results provide insights into H2 signaling and its functions in plant metabolism.

IMA peptides function in iron homeostasis and cadmium resistance

Iron (Fe), an essential micronutrient, participates in photosynthesis, respiration, and many other enzymatic reactions. Cadmium (Cd), by contrast, is a toxic element to virtually all living organisms. Both Fe deficiency and Cd toxicity severally impair crop growth and productivity, finally leading to human health issues. Understanding how plants control the uptake and homeostasis of Fe and combat Cd toxicity thus is mandatory to develop Fe-enriched but Cd-cleaned germplasms for human beings. Recent studies in Arabidopsis and rice have revealed that IRON MAN (IMA) peptides stand out as a key regulator to respond to Fe deficiency by competitively interacting with a ubiquitin E3 ligase, thus inhibiting the degradation of IVc subgroup bHLH transcription factors (TFs), mediated by 26 S proteasome. Elevated expression of IMA confers tolerance to Cd stress in both Arabidopsis and wheat by activating the iron deficiency response. Here, we discuss recent breakthroughs that IMA peptides function in the Fe-deficiency response to attain Fe homeostasis and combat Cd toxicity as a potential candidate for phytoremediation.

Genome-Wide Investigation and Expression Analysis of the Catalase Gene Family in Oat Plants (Avena sativa L.)

Through the degradation of reactive oxygen species (ROS), different antioxidant enzymes, such as catalase (CAT), defend organisms against oxidative stress. These enzymes are crucial to numerous biological functions, like plant development and defense against several biotic and abiotic stresses. However, despite the major economic importance of Avena sativa around the globe, little is known about the CAT gene's structure and organization in this crop. Thus, a genome-wide investigation of the CAT gene family in oat plants has been carried out to characterize the potential roles of those genes under different stressors. Bioinformatic approaches were used in this study to predict the AvCAT gene's structure, secondary and tertiary protein structures, physicochemical properties, phylogenetic tree, and expression profiling under diverse developmental and biological conditions. A local Saudi oat variety (AlShinen) was used in this work. Here, ten AvCAT genes that belong to three groups (Groups I-III) were identified. All identified CATs harbor the two conserved domains (pfam00199 and pfam06628), a heme-binding domain, and a catalase activity motif. Moreover, identified AvCAT proteins were located in different compartments in the cell, such as the peroxisome, mitochondrion, and cytoplasm. By analyzing their promoters, different cis-elements were identified as being related to plant development, maturation, and response to different environmental stresses. Gene expression analysis revealed that three different AvCAT genes belonging to three different subgroups showed noticeable modifications in response to various stresses, such as mannitol, salt, and ABA. As far as we know, this is the first report describing the genome-wide analysis of the oat catalase gene family, and these data will help further study the roles of catalase genes during stress responses, leading to crop improvement.

New Insights into Radio-Resistance Mechanism Revealed by (Phospho)Proteome Analysis of Deinococcus Radiodurans after Heavy Ion Irradiation

Deinococcus radiodurans (D. radiodurans) can tolerate various extreme environments including radiation. Protein phosphorylation plays an important role in radiation resistance mechanisms; however, there is currently a lack of systematic research on this topic in D. radiodurans. Based on label-free (phospho)proteomics, we explored the dynamic changes of D. radiodurans under various doses of heavy ion irradiation and at different time points. In total, 2359 proteins and 1110 high-confidence phosphosites were identified, of which 66% and 23% showed significant changes, respectively, with the majority being upregulated. The upregulated proteins at different states (different doses or time points) were distinct, indicating that the radio-resistance mechanism is dose- and stage-dependent. The protein phosphorylation level has a much higher upregulation than protein abundance, suggesting phosphorylation is more sensitive to irradiation. There were four distinct dynamic changing patterns of phosphorylation, most of which were inconsistent with protein levels. Further analysis revealed that pathways related to RNA metabolism and antioxidation were activated after irradiation, indicating their importance in radiation response. We also screened some key hub phosphoproteins and radiation-responsive kinases for further study. Overall, this study provides a landscape of the radiation-induced dynamic change of protein expression and phosphorylation, which provides a basis for subsequent functional and applied studies.

A novel benzothiophene incorporated Schiff base acting as a "turn-on" sensor for the selective detection of Serine in organic medium

A novel fluorogenic sensor N-benzo[b]thiophen-2-yl-methylene-4,5-dimethyl-benzene-1,2-diamine (BTMPD) was synthesized and characterized by using spectroscopic methods including UV-visible, FT-IR, 1H NMR, 13C NMR, and mass spectrometry. The designed fluorescent probe, owing to its remarkable properties, behaves as an efficient turn-on sensor for the sensing of amino acid Serine (Ser). Also, the strength of the probe enhances upon the addition of Ser via charge transfer, and the renowned properties of the fluorophore were duly found. The sensor BTMPD shows incredible execution potential with respect to key performance indicators such as high selectivity, sensitivity, and low detection limit. The concentration change was linear ranging from 5 × 10-8 M to 3 × 10-7 M, which is an indication of the low detection limit of 1.74 ± 0.02 nM under optimal reaction conditions. Interestingly, the Ser addition leads to an increased intensity of the probe at λ = 393 nm which other co-existing species did not. The information about the arrangement and the features of the system and the HOMO-LUMO energy levels was found out theoretically using DFT calculations which is fairly in good agreement with the experimental cyclic voltammetry results. The fluorescence sensing using the synthesized compound BTMPD reveals the practical applicability and its application in real sample analysis.

Iron Nutrition in Plants: Towards a New Paradigm?

Iron (Fe) is an essential micronutrient for plant growth and development. Fe availability affects crops' productivity and the quality of their derived products and thus human nutrition. Fe is poorly available for plant use since it is mostly present in soils in the form of insoluble oxides/hydroxides, especially at neutral to alkaline pH. How plants cope with low-Fe conditions and acquire Fe from soil has been investigated for decades. Pioneering work highlighted that plants have evolved two different strategies to mine Fe from soils, the so-called Strategy I (Fe reduction strategy) and Strategy II (Fe chelation strategy). Strategy I is employed by non-grass species whereas graminaceous plants utilize Strategy II. Recently, it has emerged that these two strategies are not fully exclusive and that the mechanism used by plants for Fe uptake is directly shaped by the characteristics of the soil on which they grow (e.g., pH, oxygen concentration). In this review, recent findings on plant Fe uptake and the regulation of this process will be summarized and their impact on our understanding of plant Fe nutrition will be discussed.