Polarization of IRON-REGULATED TRANSPORTER 1 (IRT1) to the plant-soil interface plays crucial role in metal homeostasis

Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress

Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.

TRAF proteins as key regulators of plant development and stress responses

Tumor necrosis factor receptor-associated factor (TRAF) proteins are conserved in higher eukaryotes and play key roles in transducing cellular signals across different organelles. They are characterized by their C-terminal region (TRAF-C domain) containing seven to eight anti-parallel β-sheets, also known as the meprin and TRAF-C homology (MATH) domain. Over the past few decades, significant progress has been made toward understanding the diverse roles of TRAF proteins in mammals and plants. Compared to other eukaryotic species, the Arabidopsis thaliana and rice (Oryza sativa) genomes encode many more TRAF/MATH domain-containing proteins; these plant proteins cluster into five classes: TRAF/MATH-only, MATH-BPM, MATH-UBP (ubiquitin protease), Seven in absentia (SINA), and MATH-Filament and MATH-PEARLI-4 proteins, suggesting parallel evolution of TRAF proteins in plants. Increasing evidence now indicates that plant TRAF proteins form central signaling networks essential for multiple biological processes, such as vegetative and reproductive development, autophagosome formation, plant immunity, symbiosis, phytohormone signaling, and abiotic stress responses. Here, we summarize recent advances and highlight future prospects for understanding on the molecular mechanisms by which TRAF proteins act in plant development and stress responses.

Root-to-shoot iron partitioning in Arabidopsis requires IRON-REGULATED TRANSPORTER1 (IRT1) protein but not its iron(II) transport function

IRON-REGULATED TRANSPORTER1 (IRT1) is the root high-affinity ferrous iron (Fe) uptake system and indispensable for the completion of the life cycle of Arabidopsis thaliana without vigorous Fe supplementation. Here we provide evidence supporting a second role of IRT1 in root-to-shoot partitioning of Fe. We show that irt1 mutants overaccumulate Fe in roots, most prominently in the cortex of the differentiation zone in irt1-2, compared to the wild type. Shoots of irt1-2 are severely Fe-deficient according to Fe content and marker transcripts, as expected. We generated irt1-2 lines producing IRT1 mutant variants carrying single amino-acid substitutions of key residues in transmembrane helices IV and V, Ser206 and His232, which are required for transport activity in yeast. Root short-term ⁵⁵ Fe uptake rates were uninformative concerning IRT1-mediated transport. Overall irt1-like concentrations of the secondary substrate Mn suggested that the transgenic Arabidopsis lines also remain incapable of IRT1-mediated root Fe uptake. Yet, IRT1_S206A partially complements rosette dwarfing and leaf chlorosis of irt1-2, as well as root-to-shoot Fe partitioning and gene expression defects of irt1-2, all of which are fully complemented by wild-type IRT1. Taken together, these results suggest a regulatory function for IRT1 in root-to-shoot Fe partitioning that does not require Fe transport activity of IRT1. Among the genes of which transcript levels are partially dependent on IRT1, we identify MYB DOMAIN PROTEIN10, MYB DOMAIN PROTEIN72 and NICOTIANAMINE SYNTHASE4 as candidates for effecting IRT1-dependent Fe mobilization in roots. Understanding the biological functions of IRT1 will help to improve Fe nutrition and the nutritional quality of agricultural crops.

Root-to-shoot iron partitioning in Arabidopsis requires IRON-REGULATED TRANSPORTER1 (IRT1) protein but not its iron(II) transport function

IRON-REGULATED TRANSPORTER1 (IRT1) is the root high-affinity ferrous iron (Fe) uptake system and indispensable for the completion of the life cycle of Arabidopsis thaliana without vigorous Fe supplementation. Here we provide evidence supporting a second role of IRT1 in root-to-shoot partitioning of Fe. We show that irt1 mutants overaccumulate Fe in roots, most prominently in the cortex of the differentiation zone in irt1-2, compared to the wild type. Shoots of irt1-2 are severely Fe-deficient according to Fe content and marker transcripts, as expected. We generated irt1-2 lines producing IRT1 mutant variants carrying single amino-acid substitutions of key residues in transmembrane helices IV and V, Ser206 and His232, which are required for transport activity in yeast. Root short-term ⁵⁵ Fe uptake rates were uninformative concerning IRT1-mediated transport. Overall irt1-like concentrations of the secondary substrate Mn suggested that the transgenic Arabidopsis lines also remain incapable of IRT1-mediated root Fe uptake. Yet, IRT1_S206A partially complements rosette dwarfing and leaf chlorosis of irt1-2, as well as root-to-shoot Fe partitioning and gene expression defects of irt1-2, all of which are fully complemented by wild-type IRT1. Taken together, these results suggest a regulatory function for IRT1 in root-to-shoot Fe partitioning that does not require Fe transport activity of IRT1. Among the genes of which transcript levels are partially dependent on IRT1, we identify MYB DOMAIN PROTEIN10, MYB DOMAIN PROTEIN72 and NICOTIANAMINE SYNTHASE4 as candidates for effecting IRT1-dependent Fe mobilization in roots. Understanding the biological functions of IRT1 will help to improve Fe nutrition and the nutritional quality of agricultural crops.

FYVE2, a phosphatidylinositol 3-phosphate effector, interacts with the COPII machinery to control autophagosome formation in Arabidopsis

Autophagy is an intracellular trafficking mechanism by which cytosolic macromolecules and organelles are sequestered into autophagosomes for degradation inside the vacuole. In various eukaryotes including yeast, metazoans, and plants, the precursor of the autophagosome, termed the phagophore, nucleates in the vicinity of the endoplasmic reticulum (ER) with the participation of phosphatidylinositol 3-phosphate (PI3P) and the coat protein complex II (COPII). Here we show that Arabidopsis thaliana FYVE2, a plant-specific PI3P-binding protein, provides a functional link between the COPII machinery and autophagy. FYVE2 interacts with the small GTPase Secretion-associated Ras-related GTPase 1 (SAR1), which is essential for the budding of COPII vesicles. FYVE2 also interacts with ATG18A, another PI3P effector on the phagophore membrane. Fluorescently tagged FYVE2 localized to autophagic membranes near the ER and was delivered to vacuoles. SAR1 fusion proteins were also targeted to the vacuole via FYVE2-dependent autophagy. Either mutations in FYVE2 or the expression of dominant-negative mutant SAR1B proteins resulted in reduced autophagic flux and the accumulation of autophagic organelles. We propose that FYVE2 regulates autophagosome biogenesis through its interaction with ATG18A and the COPII machinery, acting downstream of ATG2.

Microbial enhancement of plant nutrient acquisition

Nutrient availability is a determining factor for crop yield and quality. While fertilization is a major approach for improving plant nutrition, its efficacy can be limited and the production and application of fertilizers frequently bring problems to the environment. A large number of soil microbes are capable of enhancing plant nutrient acquisition and thereby offer environmentally benign solutions to meet the requirements of plant nutrition. Herein we provide summations of how beneficial microbes enhance plant acquisition of macronutrients and micronutrients. We also review recent studies on nutrition-dependent plant-microbe interactions, which highlight the plant's initiative in establishing or deterring the plant-microbe association. By dissecting complex signaling interactions between microbes within the root microbiome, a greater understanding of microbe-enhanced plant nutrition under specific biotic and abiotic stresses will be possible.

Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models

To ensure optimal utilization and bioavailability, iron uptake, transport, subcellular localization, and assimilation are tightly regulated in plants. Herein, we examine recent advances in our understanding of cellular responses to Fe deficiency. We then use intracellular mechanisms of Fe homeostasis to discuss how formalizing cell biology knowledge via a mathematical model can advance discovery even when quantitative data is limited. Using simulation-based inference to identify plausible systems mechanisms that conform to known emergent phenotypes can yield novel, testable hypotheses to guide targeted experiments. However, this approach relies on the accurate encoding of domain-expert knowledge in exploratory mathematical models. We argue that this would be facilitated by fostering more "systems thinking" life scientists and that diversifying your research team may be a practical path to achieve that goal.

A quick journey into the diversity of iron uptake strategies in photosynthetic organisms

Iron (Fe) is involved in multiple processes that contribute to the maintenance of the cellular homeostasis of all living beings. In photosynthetic organisms, Fe is notably required for photosynthesis. Although iron is generally abundant in the environment, it is frequently poorly bioavailable. This review focuses on the molecular strategies that photosynthetic organisms have evolved to optimize iron acquisition, using Arabidopsis thaliana, rice (Oryza sativa), and some unicellular algae as models. Non-graminaceous plants, including Arabidopsis, take up iron from the soil by an acidification-reduction-transport process (strategy I) requiring specific proteins that were recently shown to associate in a dedicated complex. On the other hand, graminaceous plants, such as rice, use the so-called strategy II to acquire iron, which relies on the uptake of Fe³⁺ chelated by phytosiderophores that are secreted by the plant into the rhizosphere. However, apart these main strategies, accessory mechanisms contribute to robust iron uptake in both Arabidopsis and rice. Unicellular algae combine reductive and non-reductive mechanisms for iron uptake and present important specificities compared to land plants. Since the majority of the molecular actors required for iron acquisition in algae are not conserved in land plants, questions arise about the evolution of the Fe uptake processes upon land colonization.

TpIRT1 from Polish wheat (Triticum polonicum L.) enhances the accumulation of Fe, Mn, Co, and Cd in Arabidopsis

Uptake and internal transport of micronutrients are essential for plant growth, development, and yield. In this regard, Iron Regulated Transporters (IRTs) from the Zinc Regulated Transporter (ZRT)/IRT-related protein (ZIP) family play an important role in transition metal uptake. Most studies have been focused on IRT1-like proteins in diploid species. Information on IRT1-like proteins in polyploids is limited. Here, we studied the function of TpIRT1A and TpIRT1B homoeologs in a tetraploid crop, Polish wheat (Triticum polonicum L.). Our results highlighted the importance of TpIRT1 in mediating the uptake and translocation of Fe, Mn, Co, and Cd with direct implications for wheat yield potential. Both TpIRT1A and TpIRT1B were located at the plasma membrane and internal vesicle-like organelle in protoplasts of Arabidopsis thaliana L. and increased Cd and Co sensitivity in yeast. The over-expression of TpIRT1B in A. thaliana increased Fe, Mn, Co, and Cd concentration in its tissues and improved plant growth under Fe, Mn, and Co deficiencies, while increased the sensitivity to Cd compared to wild type. Functional analysis of IRT1 homoeologs from tetraploid and diploid ancestral wheat species in yeast disclosed four distinct amino acid residues in TdiIRT1B (T. dicoccum L. (Schrank)) and TtuIRT1B (T. turgidum L.). Together, our results increase the knowledge of IRT1 function in a globally important crop, wheat.

Aluminium, Iron and Silicon Subcellular Redistribution in Wheat Induced by Manganese Toxicity

Acidic soils can promote the bioavailability of Al, Mn, and Fe to toxic levels, reducing crop growth and productivity. Symptoms of metal excess/deficit are dependent on the chemical composition of the soil solution and of plant tissues. In the present study, the concentration and subcellular distribution of Al, Mn, Fe, and Si (known to alleviate metal stress) were quantified through inductively coupled plasma mass spectrometry (ICP-MS) in roots and shoots of wheat grown in acidic soils with rising levels of Mn. In control acidic soil, wheat showed high concentrations of Al, Mn, and Fe. After Mn supplementation, bioavailable Al, Fe, and Si levels increased in the soil solution, but plant uptake ratio decreased. Root Mn levels increased, while those of Al, Fe, and Si decreased. Although elements were increasingly translocated to the shoot, root Al and Fe concentrations were 10-fold higher than those in the shoot. At the highest Mn concentration supplied, Al, Fe, and Si proportions increased in the organelles, while Mn proportion increased in the vacuole. High bioavailable Mn levels disrupt metal homeostasis in wheat grown in acidic soils, influencing element subcellular distribution. Symptoms of metal toxicity result from interactions between several elements, and therefore a comprehensive chemical analysis of soil solution and plant tissues contributes to a more accurate understanding of their uptake dynamics and their agronomic implications.

Specific expression of AtIRT1 in phloem companion cells suggests its role in iron translocation in aboveground plant organs

IRON-REGULATED TRANSPORTER 1 (IRT1) is a central iron transporter responsible for the uptake of iron from the rhizosphere to root epidermal cells. This study uses immunohistochemistry, histochemistry, and fluorometry to show that this gene's promoter is also active in the aboveground parts, specifically in phloem companied cells. Promoter activity here was regulated by iron as it was in the roots. The promoter of the close IRT2 homolog was root-specific and only weakly active in the stem pits. RT-PCR showed the presence of a long splicing form exclusively in iron-deficient roots. The short splicing form was present in all organs regardless of the presence of iron. Immunohistology exhibited labeling on the periphery of the epidermal cells in matured root zone and intracellular patches in the meristematic cells. In the aboveground organs, the protein was seen in the whole volume of companion cells and in neighboring sieve elements as bodies. The fluorescent protein technique revealed the short IRT1 form to be present in the patches accumulated mainly around the nucleus and the long form as a continuous layer along the cells periphery. These results suggest that IRT1 has a role also in the aboveground organs.

Autophagy Mediates the Degradation of Plant ESCRT Component FREE1 in Response to Iron Deficiency

Multivesicular body (MVB)-mediated endosomal sorting and macroautophagy are the main pathways mediating the transport of cellular components to the vacuole and are essential for maintaining cellular homeostasis. The interplay of these two pathways remains poorly understood in plants. In this study, we show that FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1), which was previously identified as a plant-specific component of the endosomal sorting complex required for transport (ESCRT), essential for MVB biogenesis and plant growth, can be transported to the vacuole for degradation in response to iron deficiency. The vacuolar transport of ubiquitinated FREE1 protein is mediated by the autophagy pathway. As a consequence, the autophagy deficient mutants, atg5-1 and atg7-2, accumulate more endogenous FREE1 protein and display hypersensitivity to iron deficiency. Furthermore, under iron-deficient growth condition autophagy related genes are upregulated to promote the autophagic degradation of FREE1, thereby possibly relieving the repressive effect of FREE1 on iron absorption. Collectively, our findings demonstrate a unique regulatory mode of protein turnover of the ESCRT machinery through the autophagy pathway to respond to iron deficiency in plants.

Lsi2: A black box in plant silicon transport

BACKGROUND

Silicon (Si) is widely considered a non-essential but beneficial element for higher plants, providing broad protection against various environmental stresses (both biotic and abiotic), particularly in species that can readily absorb the element. Two plasma-membrane proteins are known to coordinate the radial transport of Si (in the form of Si(OH)4) from soil to xylem within roots: the influx channel Lsi1 and the efflux transporter Lsi2. From a structural and mechanistic perspective, much more is known about Lsi1 (a member of the NIP-III subgroup of the Major Intrinsic Proteins) compared to Lsi2 (a putative Si(OH)4/H+ antiporter, with some homology to bacterial anion transporters).

SCOPE

Here, we critically review the current state of understanding regarding the physiological role and molecular characteristics of Lsi2. We demonstrate that the structure-function relationship of Lsi2 is largely uncharted and that the standing transport model requires much better supportive evidence. We also provide (to our knowledge) the most current and extensive phylogenetic analysis of Lsi2 from all fully sequenced higher-plant genomes. We end by suggesting research directions and hypotheses to elucidate the properties of Lsi2.

CONCLUSIONS

Given that Lsi2 is proposed to mediate xylem Si loading and thus root-to-shoot translocation and biosilicification, it is imperative that the field of Si transport focus its efforts on a better understanding of this important topic. With this review, we aim to stimulate and advance research in the field of Si transport and thus better exploit Si to improve crop resilience and agricultural output.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11104-021-05061-1.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

Osteoblast iron genes: real time PCR and microarray hybridization approach under hyperoxia

OBJECTIVES

Iron is essential for cell growth, differentiation, electron transfer, and oxygen transport. Hyperoxia may increase the turnover of bone matrix components with a net effect of accelerated bone growth. Although hyperoxia was claimed could increase osteoblast activity, but expression level in possible genes which play role in proliferation is still unclear. This research aims to prove the differences of expression level of transferrin receptor gene and iron regulated transporter and other genes of 7F2 under 24 h normoxia, 24 h hyperoxia, and 48 h hyperoxia and the effect of hyperoxia by using osteoblast cell culture 7F₂.

METHODS

Reverse transcriptase, real time Polymerase Chain Reaction (PCR), and microarray is used to qualitatively detect gene expression. The computer softwares such as National Center for Biotechnology Information (NCBI) data base, Software Affymetrix, DNA Strider program, Genomatix - DiAlign program, Oligo 5.0 program (Software primer design) from Wojciech & Piotr Rychlik, and Genetyx-Mac version 8.0 have been used to analyze the PCR result.

RESULTS

Under 24 h hyperoxia, there were 3,884 copies of transferrin receptor mRNA per 1,000,000 copies of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) mRNA. After 24 h hyperoxia, 8,325 copies of transferrin receptor mRNA per 1,000,000 GAPDH mRNA copies were found showing 2.1-fold up regulation. After 48 h hyperoxia, there was no significant increase at the level of expression of transferrin receptor mRNA, 8,079 mRNA copies per 1,000,000 copies of mRNA were found (2.0-fold up regulation compared with 24 h normoxia).

CONCLUSIONS

It can be concluded that hyperoxia might have an effect on upregulating the expression of some osteoblast genes which might have an impact on osteoblast activity.

Manganese triggers phosphorylation-mediated endocytosis of the Arabidopsis metal transporter NRAMP1

The NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 1 (NRAMP1) transporter guarantees plant survival of manganese (Mn) deficiency by mediating Mn entry into root cells. Unlike other high-affinity metal transporters, NRAMP1 is only slightly regulated at the transcriptional level. We show here that adequate Mn content in tissues is safeguarded through a tight control of the quantity of NRAMP1 present at the surface of root cells. Depending on Mn availability, an NRAMP1-GFP fusion protein cycles dynamically between the plasma membrane (PM) and endosomal compartments. This involves a clathrin-mediated endocytosis pathway, as disrupting this pathway in auxilin-overexpressor lines prevents NRAMP1 internalization. Mutation of the phosphorylated serine residues 20, 22 and 24 in the cytosol-exposed N terminus of NRAMP1 alters its membrane distribution. Indeed, a phospho-dead mutation stabilizes NRAMP1 at the PM, regardless of the Mn regime, and dramatically reduces plant tolerance to Mn toxicity. Conversely a phosphomimetic mutant is constitutively internalized into endosomes. Together, these data establish that phosphorylation of NRAMP1 is the trigger for its Mn-induced endocytosis and represents the main level of regulation of this transporter. Furthermore, the extent of Mn toxicity observed when interrupting NRAMP1 membrane cycling undermines the dogma that Mn is only marginally toxic to plants.

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.

Root hairs: the villi of plants

Strikingly, evolution shaped similar tubular structures at the µm to mm scale in roots of sessile plants and in small intestines of mobile mammals to ensure an efficient transfer of essential nutrients from 'dead matter' into biota. These structures, named root hairs (RHs) in plants and villi in mammals, numerously stretch into the environment, and extremely enlarge root and intestine surfaces. They are believed to forage for nutrients, and mediate their uptake. While the conceptional understanding of plant RH function in hydromineral nutrition seems clear, experimental evidence presented in textbooks is restricted to a very limited number of reference-nutrients. Here, we make an element-by-element journey through the periodic table and link individual nutrient availabilities to the development, structure/shape and function of RHs. Based on recent developments in molecular biology and the identification of mutants differing in number, length or other shape-related characteristics of RHs in various plant species, we present comprehensive advances in (i) the physiological role of RHs for the uptake of specific nutrients, (ii) the developmental and morphological responses of RHs to element availability and (iii) RH-localized nutrient transport proteins. Our update identifies crucial roles of RHs for hydromineral nutrition, mostly under nutrient and/or water limiting conditions, and highlights the influence of certain mineral availabilities on early stages of RH development, suggesting that nutritional stimuli, as deficiencies in P, Mn or B, can even dominate over intrinsic developmental programs underlying RH differentiation.

Attracted to membranes: lipid-binding domains in plants

Membranes are essential for cells and organelles to function. As membranes are impermeable to most polar and charged molecules, they provide electrochemical energy to transport molecules across and create compartmentalized microenvironments for specific enzymatic and cellular processes. Membranes are also responsible for guided transport of cargoes between organelles and during endo- and exocytosis. In addition, membranes play key roles in cell signaling by hosting receptors and signal transducers and as substrates and products of lipid second messengers. Anionic lipids and their specific interaction with target proteins play an essential role in these processes, which are facilitated by specific lipid-binding domains. Protein crystallography, lipid-binding studies, subcellular localization analyses, and computer modeling have greatly advanced our knowledge over the years of how these domains achieve precision binding and what their function is in signaling and membrane trafficking, as well as in plant development and stress acclimation.

The many facets of protein ubiquitination and degradation in plant root iron-deficiency responses

Organisms need to deal with the absolute requirement for metals and also their possible toxicity. This is achieved through an intricate network of signaling pathways that are integrated to ultimately fine-tune iron uptake and metabolism. The mechanisms by which plants cope with iron limitation and the associated genomic responses are well characterized. On top of this transcriptional cascade is another level of regulation involving the post-translational protein modification and degradation. The ubiquitination and/or degradation of several transcription factors in the iron-deficiency signaling pathways and metal transporters has recently come to light. In this review we discuss the mechanisms and possible roles of protein modification and turnover in the regulation of root iron-deficiency responses. We also highlight the tight coupling between metal sensing by E3 ubiquitin ligases or bifunctional transporters and protein degradation.

Coordinated homeostasis of essential mineral nutrients: a focus on iron

In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.

Evidence for a role of nitric oxide in iron homeostasis in plants

Nitric oxide (NO), once regarded as a poisonous air pollutant, is now understood as a regulatory molecule essential for several biological functions in plants. In this review, we summarize NO generation in different plant organs and cellular compartments, and also discuss the role of NO in iron (Fe) homeostasis, particularly in Fe-deficient plants. Fe is one of the most limiting essential nutrient elements for plants. Plants often exhibit Fe deficiency symptoms despite sufficient tissue Fe concentrations. NO appears to not only up-regulate Fe uptake mechanisms but also makes Fe more bioavailable for metabolic functions. NO forms complexes with Fe, which can then be delivered into target cells/tissues. NO generated in plants can alleviate oxidative stress by regulating antioxidant defense processes, probably by improving functional Fe status and by inducing post-translational modifications in the enzymes/proteins involved in antioxidant defense responses. It is hypothesized that NO acts in cooperation with transcription factors such as bHLHs, FIT, and IRO to regulate the expression of enzymes and proteins essential for Fe homeostasis. However, further investigations are needed to disentangle the interaction of NO with intracellular target molecules that leads to enhanced internal Fe availability in plants.

Specificity and Plasticity of the Functional Ionome of Brassica napus and Triticum aestivum Exposed to Micronutrient or Beneficial Nutrient Deprivation and Predictive Sensitivity of the Ionomic Signatures

The specific variation in the functional ionome was studied in Brassica napus and Triticum aestivum plants subjected to micronutrient or beneficial mineral nutrient deprivation. Effects of these deprivations were compared to those of macronutrient deprivation. In order to identify early events, plants were harvested after 22 days, i.e., before any significant reduction in growth relative to control plants. Root uptake, tissue concentrations and relative root nutrient contents were analyzed revealing numerous interactions with respect to the 20 elements quantified. The assessment of the functional ionome under individual mineral nutrient deficiency allows the identification of a large number of interactions between elements, although it is not totally exhaustive, and gives access to specific ionomic signatures that discriminate among deficiencies in N, P, S, K, Ca, Mn, Fe, Zn, Na, Si, and Se in both species, plus Mg, Cl, Cu, and Mo in wheat. Ionome modifications and components of ionomic signatures are discussed in relation to well-known mechanisms that may explain crosstalks between mineral nutrients, such as between Na and K, V, Se, Mo and S or Fe, Zn and Cu. More surprisingly, when deprived of beneficial nutrients such as Na, Si, Co, or Se, the plant ionome was strongly modified while these beneficial nutrients contributed greatly to the leaf ionomic signature of most mineral deficiencies.

Endocytosis in plants: Peculiarities and roles in the regulated trafficking of plant metal transporters

The removal of transmembrane proteins from the plasma membrane via endocytosis has emerged as powerful strategy in the regulation of receptor signalling and molecule transport. In the last decade, IRON-REGULATED TRANSPORTER1 (IRT1) has been established as one of the key plant model proteins for studying endomembrane trafficking. The use of IRT1 and additional other metal transporters has uncovered novel factors involved in plant endocytosis and facilitated a better understanding of the role of endocytosis in the fine balancing of plant metal homoeostasis. In this review, we outline the specifics of plant endocytosis compared to what is known in yeast and mammals, and based on several examples, we demonstrate how studying metal transport has contributed to extending our knowledge of endocytic trafficking by shedding light on novel regulatory mechanisms and factors.

The root iron transporter 1 governs cadmium uptake in Vicia sativa roots

Cadmium is a non-essential element for plants and that inhibits plant growth and development. The Zhangye Mawan (ZM) variety of Vicia sativa is more sensitive to Cd toxicity than that Lanjian 3# (L3) variety, but the underlying mechanism is not fully understood. Here, we demonstrated that ZM showed higher Cd accumulation than L3 based on root Cd content and Cd fluorescence intensity in root protoplasts. VsRIT1, a member of the ZIP (ZRT/IRT-like protein) family, showed expression levels in ZM roots 8-fold higher than those in L3 roots under Cd exposure. VsRIT1 expression increased Cd transport and accumulation in Arabidopsis and yeast. These suggests that VsRIT1 participates in Cd uptake by V. sativa roots. Furthermore, ZM root tips have a higher capacity for transient Cd influx than L3 roots when exposed to Cd alone or Cd and iron (Fe) together, owing to the higher VsRIT1 expression in ZM. Our findings also imply that Cd may compete with Fe or/and zinc (Zn) for uptake via VsRIT1 in V. sativa or yeast.

Dynamic Control of the High-Affinity Iron Uptake Complex in Root Epidermal Cells

In plants, iron uptake from the soil is tightly regulated to ensure optimal growth and development. Iron absorption in Arabidopsis root epidermal cells requires the IRT1 transporter that also allows the entry of certain non-iron metals, such as Zn, Mn, and Co. Recent work demonstrated that IRT1 endocytosis and degradation are controlled by IRT1 non-iron metal substrates in a ubiquitin-dependent manner. To better understand how metal uptake is regulated, we identified IRT1-interacting proteins in Arabidopsis roots by mass spectrometry and established an interactome of IRT1. Interestingly, the AHA2 proton pump and the FRO2 reductase, both of which work in concert with IRT1 in the acidification-reduction-transport strategy of iron uptake, were part of this interactome. We confirmed that IRT1, FRO2, and AHA2 associate through co-immunopurification and split-ubiquitin analyses, and uncovered that they form tripartite direct interactions. We characterized the dynamics of the iron uptake complex and showed that FRO2 and AHA2 ubiquitination is independent of the non-iron metal substrates transported by IRT1. In addition, FRO2 and AHA2 are not largely endocytosed in response to non-iron metal excess, unlike IRT1. Indeed, we provide evidence that the phosphorylation of IRT1 in response to high levels of non-iron metals likely triggers dissociation of the complex. Overall, we propose that a dedicated iron-acquisition protein complex exists at the cell surface of Arabidopsis root epidermal cells to optimize iron uptake.

A curated list of genes that affect the plant ionome

Understanding the mechanisms underlying plants' adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements, and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.

SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling

In plants, the ubiquitin-proteasome system, endosomal sorting, and autophagy are essential for protein degradation; however, their interplay remains poorly understood. Here, we show that four Arabidopsis (Arabidopsis thaliana) E3 ubiquitin ligases, SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA1 (SINAT1), SINAT2, SINAT3, and SINAT4, regulate the stabilities of FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING1 (FREE1) and VACUOLAR PROTEIN SORTING23A (VPS23A), key components of the endosomal sorting complex required for transport-I, to modulate abscisic acid (ABA) signaling. GFP-SINAT1, GFP-SINAT2, and GFP-SINAT4 primarily localized to the endosomal and autophagic vesicles. SINATs controlled FREE1 and VPS23A ubiquitination and proteasomal degradation. SINAT overexpressors showed increased ABA sensitivity, ABA-responsive gene expression, and PYRABACTIN RESISTANCE1-LIKE4 protein levels. Furthermore, the SINAT-FREE1/VPS23A proteins were codegraded by the vacuolar pathway. In particular, during recovery post-ABA exposure, SINATs formed homo- and hetero-oligomers in vivo, which were disrupted by the autophagy machinery. Taken together, our findings reveal a novel mechanism by which the proteasomal and vacuolar turnover systems regulate ABA signaling in plants.

SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants

The endosomal sorting complex required for transport (ESCRT) machinery is an ancient, evolutionarily conserved membrane remodeling complex that is essential for multivesicular body (MVB) biogenesis in eukaryotes. FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1), which was previously identified as a plant-specific ESCRT component, modulates MVB-mediated endosomal sorting and autophagic degradation. Although the basic cellular functions of FREE1 as an ESCRT component have been described, the regulators that control FREE1 turnover remain unknown. Here, we analyzed how FREE1 homeostasis is mediated by the RING-finger E3 ubiquitin ligases, SINA of Arabidopsis thaliana (SINATs), in response to iron deficiency. Under iron-deficient growth conditions, SINAT1-4 were induced and ubiquitinated FREE1, thereby promoting its degradation and relieving the repressive effect of FREE1 on iron absorption. By contrast, SINAT5, another SINAT member that lacks ubiquitin ligase activity due to the absence of the RING domain, functions as a protector protein which stabilizes FREE1. Collectively, our findings uncover a hitherto unknown mechanism of homeostatic regulation of FREE1, and demonstrate a unique regulatory SINAT-FREE1 module that subtly regulates plant response to iron deficiency stress.

Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis

Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and intercellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how CME functions in planta To facilitate the direct quantitative study of plant CME, we review current routinely used methods and present refined, standardized quantitative imaging protocols that allow the detailed characterization of CME at multiple scales in plant tissues. These protocols include: (1) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultrastructure of clathrin-coated vesicles; (2) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (3) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (4) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.This article has an associated First Person interview with the first author of the paper.

ESCRT-I Component VPS23A Sustains Salt Tolerance by Strengthening the SOS Module in Arabidopsis

The Salt-Overly-Sensitive (SOS) signaling module, comprising the sodium-transport protein SOS1 and the regulatory proteins SOS2 and SOS3, is well known as the central salt excretion system, which helps protect plants against salt stress. Here we report that VPS23A, a component of the ESCRT (endosomal sorting complex required for transport), plays an essential role in the function of the SOS module in conferring plant salt tolerance. VPS23A enhances the interaction of SOS2 and SOS3. In the presence of salt stress, VPS23A positively regulates the redistribution of SOS2 to the plasma membrane, which then activates the antiporter activity of SOS1 to reduce Na⁺ accumulation in plant cells. Genetic evidence demonstrated that plant salt tolerance achieved by the overexpression of SOS2 and SOS3 dependeds on VPS23A. Taken together, our results revealed that VPS23A is a crucial regulator of the SOS module and affects the localization of SOS2 to the cell membrane. Moreover, the strong salt tolerance of Arabidopsis seedlings conferred by the engineered membrane-bound SOS2 revealed the significance of SOS2 sorting to the cell membrane in achieving its function, providing a potential strategy for crop salt tolerance engineering.

Subcellular Localization of PI3P in Arabidopsis

Phosphatidylinositol-3-phosphate (PI3P) is a signaling phospholipid enriched in the membranes of late endosomes (LE) and vacuoles. PI3P mediates vacuolar and endosomal trafficking through recruiting PI3P-binding effector proteins to the LE. PI3P is produced from phosphatidylinositol by the PI 3-kinase complex containing VACUOLAR PROTEIN SORTING 34 (VPS34). The role of PI3P has been elucidated by using genetically encoded PI3P biosensors. We previously showed that Arabidopsis VPS38, a component of the VPS34 complex, localized at the LE and that VPS38 is essential for proper PI3P distribution in endosomal and vacuolar trafficking routes. In this chapter, we describe methods for microscopic imaging of PI3P using the PI3P biosensor citrine-2 × FYVE and the PI 3-kinase inhibitors.

The effect of ABRE BINDING FACTOR 4-mediated FYVE1 on salt stress tolerance in Arabidopsis

FYVE1 encodes a protein that is localized to the peripheral membrane of late endosomal compartments, and is involved in the regulation of mulitivesicular/prevacuolar compartment protein sorting. It was found that FYVE1 attenuates ABA signaling through degrading ABA receptors PYR1 and PYL4 by ESCRT pathway, and also interacts with transcription factors ABF4 and ABI5 to transcriptionally inhibit ABA signaling pathway by reducing their binding to the cis-regulatory sequences of their downstream genes. However, the mechanisms underlying the transcriptional regulation of FYVE1 and its biological function in salt stress are largely unknown. Here, we show that fyve1 knockdown-mutants show enhanced tolerance to salt stress, while overexpression of FYVE1 results in increased sensitivity to salt stress. Further analysis shows that FYVE1 negatively regulates salt stress tolerance, which is associated with ABA signaling pathway. ABRE BINDING FACTOR 4 (ABF4) directly binds to promoter of FYVE1 to activate its transcription. Moreover, FYVE1 interacts with and promotes degradation of all ABA PYR/PYL receptors. Thus, our results suggest that FYVE1 negatively modulates salt stress tolerance in Arabidopsis via a negative feedback loop.

Alteration of iron responsive gene expression in Arabidopsis glutaredoxin S17 loss of function plants with or without iron stress

Iron (Fe) is a mineral nutrient and a metal cofactor essential for plants. Iron limitation can have detrimental effects on plant growth and development, while excess iron inside plant cells leads to oxidative damage. As a result, plants have evolved complex regulatory networks to respond to fluctuations in cellular iron concentrations. The mechanisms that regulate these responses however, are not fully understood. Heterologous expression of an Arabidopsis thaliana monothiol glutaredoxin S17 (GRXS17) suppresses the over-accumulation of iron in the Saccharomyces cerevisiae Grx3/Grx4 mutant and disruption of GRXS17 causes plant sensitivity to exogenous oxidants and iron deficiency stress. GRXS17 may act as an important regulator in the plant's ability to respond to iron deficiency stress and maintain redox homeostasis. Here, we extend this investigation by analyzing iron-responsive gene expression of the Fer-like iron deficiency-induced transcription factor (FIT) network (FIT, IRT1, FRO1, and FRO2) and the bHLH transcription factor POPEYE (PYE) network (PYE, ZIF1, FRO3, NAS4, and BTS) in GRXS17 KO plants and wildtype controls grown under iron sufficiency and deficiency conditions. Our findings suggest that GRXS17 is required for tolerance to iron deficiency, and plays a negative regulatory role under conditions of iron sufficiency.

The importance of being edgy: cell geometric edges as an emerging polar domain in plant cells

Polarity is an essential feature of multicellular organisms and underpins growth and development as well as physiological functions. In polyhedral plant cells, polar domains at different faces have been studied in detail. In recent years, cell edges (where two faces meet) have emerged as discrete spatial domains with distinct biochemical identities. Here, we review and discuss recent advances in our understanding of cell edges as functional polar domains in plant cells and other organisms, highlighting conceptual parallels and open questions regarding edge polarity.

Plant Cell Polarity: Creating Diversity from Inside the Box

Cell polarity in plants operates across a broad range of spatial and temporal scales to control processes from acute cell growth to systemic hormone distribution. Similar to other eukaryotes, plants generate polarity at both the subcellular and tissue levels, often through polarization of membrane-associated protein complexes. However, likely due to the constraints imposed by the cell wall and their extremely plastic development, plants possess novel polarity molecules and mechanisms highly tuned to environmental inputs. Considerable progress has been made in identifying key plant polarity regulators, but detailed molecular understanding of polarity mechanisms remains incomplete in plants. Here, we emphasize the striking similarities in the conceptual frameworks that generate polarity in both animals and plants. To this end, we highlight how novel, plant-specific proteins engage in common themes of positive feedback, dynamic intracellular trafficking, and posttranslational regulation to establish polarity axes in development. We end with a discussion of how environmental signals control intrinsic polarity to impact postembryonic organogenesis and growth.

TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants

Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.

Toxic levels of manganese in an acidic Cambisol alters antioxidant enzymes activity, element uptake and subcellular distribution in Triticum aestivum

In the Montado system, in Portuguese Alentejo region, some Eutric Cambisols are known to promote manganese (Mn) toxicity in wheat. Variation on bioavailable Mn concentration depends on soil acidity, which can be increased by natural events (e.g. waterlogging) or human activity (e.g. excess use of chemical fertilizers). The effect of increasing soil Mn on crop element uptake, element distribution and oxidative stress was evaluated on winter wheat (Triticum aestivum). Plants were grown for 3 weeks in an acidic Cambisol spiked with increasing Mn concentrations (0, 45.2 and 90.4 mg MnCl₂/Kg soil). Calcium (Ca), phosphorus (P), magnesium (Mg) and Mn were quantified in the soil solution, root and shoot tissues and respective subcellular fractions. The activity of the antioxidant enzymes ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), guaiacol peroxidase (GPX) and superoxide dismutase (SOD) were determined in extracts of wheat shoots and roots. Overall, increase in soil bioavailable Mn inhibited the uptake of other elements, increased the Ca proportion in the root apoplast, promoted the translocation of Mn and P to shoot tissues and increased their proportion in the shoot vacuoles. Wheat roots showed greater antioxidant enzymes activities than shoots. These activities decreased at the highest soil Mn concentration in both plant parts. Wheat roots appear to be more sensitive to oxidative stress derived from excess soil Mn and promote Mn translocation and storage in shoot vacuoles, probably in Mn and P complexes, as a detoxification strategy. Improvement in wheat production, in acidic soils, may rely on the enhancement of its Mn detoxification strategies.

Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens

Genome-wide identification, together with gene expression patterns and promoter region analysis of FYVE and PHOX proteins in Physcomitrella patens, emphasized their importance in regulating mainly developmental processes in P. patens. Phosphatidylinositol 3-phosphate (PtdIns3P) is a signaling phospholipid, which regulates several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through effector proteins have been partially explored in plants, with main focus on Arabidopsis thaliana. In this study, we searched for genes coding for PtdIns3P-binding proteins such as FYVE and PHOX domain-containing sequences from different photosynthetic organisms to gather evolutionary insights on these phosphoinositide binding domains, followed by an in silico characterization of the FYVE and PHOX gene families in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor (TF) binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2 to 3D growth. These studies would identify ancestral regulatory players undertaken during plant evolution.

The Beginning of the End: Initial Steps in the Degradation of Plasma Membrane Proteins

The plasma membrane (PM), as border between the inside and the outside of a cell, is densely packed with proteins involved in the sensing and transmission of internal and external stimuli, as well as transport processes and is therefore vital for plant development as well as quick and accurate responses to the environment. It is consequently not surprising that several regulatory pathways participate in the tight regulation of the spatiotemporal control of PM proteins. Ubiquitination of PM proteins plays a key role in directing their entry into the endo-lysosomal system, serving as a signal for triggering endocytosis and further sorting for degradation. Nevertheless, a uniting picture of the different roles of the respective types of ubiquitination in the consecutive steps of down-regulation of membrane proteins is still missing. The trans-Golgi network (TGN), which acts as an early endosome (EE) in plants receives the endocytosed cargo, and here the decision is made to either recycled back to the PM or further delivered to the vacuole for degradation. A multi-complex machinery, the endosomal sorting complex required for transport (ESCRT), concentrates ubiquitinated proteins and ushers them into the intraluminal vesicles of multi-vesicular bodies (MVBs). Several ESCRTs have ubiquitin binding subunits, which anchor and guide the cargos through the endocytic degradation route. Basic enzymes and the mode of action in the early degradation steps of PM proteins are conserved in eukaryotes, yet many plant unique components exist, which are often essential in this pathway. Thus, deciphering the initial steps in the degradation of ubiquitinated PM proteins, which is the major focus of this review, will greatly contribute to the larger question of how plants mange to fine-tune their responses to their environment.

The roles of endomembrane trafficking in plant abiotic stress responses

Endomembrane trafficking is a fundamental cellular process in all eukaryotic cells and its regulatory mechanisms have been extensively studied. In plants, the endomembrane trafficking system needs to be constantly adjusted to adapt to the ever-changing environment. Evidence has accumulated supporting the idea that endomembrane trafficking is tightly linked to stress signaling pathways to meet the demands of rapid changes in cellular processes and to ensure the correct delivery of stress-related cargo molecules. However, the underlying mechanisms remain unknown. In this review, we summarize the recent findings on the functional roles of both secretory trafficking and endocytic trafficking in different types of abiotic stresses. We also highlight and discuss the unique properties of specific regulatory molecules beyond their conventional functions in endosomal trafficking during plant growth under stress conditions.

Remove, Recycle, Degrade: Regulating Plasma Membrane Protein Accumulation

Interactions between plant cells and the environment rely on modulation of protein receptors, transporters, channels, and lipids at the plasma membrane (PM) to facilitate intercellular communication, nutrient uptake, environmental sensing, and directional growth. These functions are fine-tuned by cellular pathways maintaining or reducing particular proteins at the PM. Proteins are endocytosed, and their fate is decided between recycling and degradation to modulate localization, abundance, and activity. Selective autophagy is another pathway regulating PM protein accumulation in response to specific conditions or developmental signals. The mechanisms regulating recycling, degradation, and autophagy have been studied extensively, yet we are just now addressing their regulation and coordination. Here, we (1) provide context concerning regulation of protein accumulation, recycling, or degradation by overviewing endomembrane trafficking; (2) discuss pathways regulating recycling and degradation in terms of cellular roles and cargoes; (3) review plant selective autophagy and its physiological significance; (4) focus on two decision-making mechanisms: regulation of recycling versus degradation of PM proteins and coordination between autophagy and vacuolar degradation; and (5) identify future challenges.

Polarized transport across root epithelia

Plant roots explore the soil to acquire water and nutrients which are often available at concentrations that drastically differ from the plant's actual need for growth and development. This stark difference between availability and requirement can be dealt with owing to the root's architecture as an inverted gut. In roots, the two epithelial characteristics (selective acquisition and diffusion barrier) are split between two cell layers: the epidermis at the root periphery and the endodermis as the innermost cortical cell layer around the vasculature. Polarized transport of nutrients across the root epithelium can be achieved through different pathways: apoplastic, symplastic, or coupled transcellular. This review highlights different features of the root that allow this polarized transport. Special emphasis is placed on the coupled transcellular pathway, facilitated by polarized nutrient carriers along root cell layers but barred by suberin lamellae in endodermal cells.

RST1 Is a FREE1 Suppressor That Negatively Regulates Vacuolar Trafficking in Arabidopsis

FYVE domain protein required for endosomal sorting1 (FREE1), a plant-specific endosomal sorting complex required for transport-I component, is essential for the biogenesis of multivesicular bodies (MVBs), vacuolar degradation of membrane protein, cargo vacuolar sorting, autophagic degradation, and vacuole biogenesis in Arabidopsis (Arabidopsis thaliana). Here, we report the characterization of RESURRECTION1 (RST1) as a suppressor of free1 that, when mutated as a null mutant, restores the normal MVB and vacuole formation of a FREE1-RNAi knockdown line and consequently allows survival. RST1 encodes an evolutionarily conserved multicellular organism-specific protein, which contains two Domain of Unknown Function 3730 domains, showing no similarity to known proteins, and predominantly localizes in the cytosol. The depletion of FREE1 causes substantial accumulation of RST1, and transgenic Arabidopsis plants overexpressing RST1 display retarded seedling growth with dilated MVBs, and inhibition of endocytosed FM4-64 dye to the tonoplast, suggesting that RST1 has a negative role in vacuolar transport. Consistently, enhanced endocytic degradation of membrane vacuolar cargoes occurs in the rst1 mutant. Further transcriptomic comparison of rst1 with free1 revealed a negative association between gene expression profiles, demonstrating that FREE1 and RST1 have antagonistic functions. Thus, RST1 is a negative regulator controlling membrane protein homeostasis and FREE1-mediated functions in plants.

Ubiquitin recognition in endocytic trafficking - with or without ESCRT-0

The ability to sense and adapt to the constantly changing environment is important for all organisms. Cell surface receptors and transporters are key for the fast response to extracellular stimuli and, thus, their abundance on the plasma membrane has to be strictly controlled. Heteromeric endosomal sorting complexes required for transport (ESCRTs) are responsible for mediating the post-translational degradation of endocytosed plasma membrane proteins in eukaryotes and are essential both in animals and plants. ESCRTs bind and sort ubiquitylated cargoes for vacuolar degradation. Although many components that comprise the multi-subunit ESCRT-0, ESCRT-I, ESCRT-II and ESCRT-III complexes are conserved in eukaryotes, plant and animal ESCRTs have diverged during the course of evolution. Homologues of ESCRT-0, which recognises ubiquitylated cargo, have emerged in metazoan and fungi but are not found in plants. Instead, the Arabidopsis genome encodes plant-specific ubiquitin adaptors and a greater number of target of Myb protein 1 (TOM1) homologues than in mammals. In this Review, we summarise and discuss recent findings on ubiquitin-binding proteins in Arabidopsis that could have equivalent functions to ESCRT-0. We further hypothesise that SH3 domain-containing proteins might serve as membrane curvature-sensing endophilin and amphiphysin homologues during plant endocytosis.

The bifunctional transporter-receptor IRT1 at the heart of metal sensing and signalling

Transporters are at the centre of regulatory modules allowing optimal assimilation, distribution or efflux of substrate molecules. The IRT1 root metal transporter represents a textbook example in which detailed regulatory networks have been shown to integrate several endogenous and exogenous cues at various levels to regulate its expression and to fine tune iron uptake. Here, we summarise recent advances in the dissection of the transcriptional and posttranslational control of IRT1 by its various metals substrates and discuss the emerging role of IRT1 in the direct sensing of non-iron metals flowing through IRT1 to drive its degradation. We propose that transporters that also act as receptors are likely to be a common theme in the regulation of nutrient transport by sensing local nutrient concentrations.

Functional characterization of Gh_A08G1120 (GH3.5) gene reveal their significant role in enhancing drought and salt stress tolerance in cotton

BACKGROUND

Auxins play an important role in plant growth and development; the auxins responsive gene; auxin/indole-3-acetic acid (Aux/IAA), small auxin-up RNAs (SAUR) and Gretchen Hagen3 (GH3) control their mechanisms. The GH3 genes function in homeostasis by the catalytic activities in auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids.

RESULTS

In our study, we identified the GH3 genes in three cotton species; Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, analyzed their chromosomal distribution, phylogenetic relationships, cis-regulatory element function and performed virus induced gene silencing of the novel Gh_A08G1120 (GH3.5) gene. The phylogenetic tree showed four clusters of genes with clade 1, 3 and 4 having mainly members of the GH3 of the cotton species while clade 2 was mainly members belonging to Arabidopsis. There were no paralogous genes, and few orthologous genes were observed between Gossypium and other species. All the GO terms were detected, but only 14 genes were found to have described GO terms in upland cotton, more biological functions were detected, as compared to the other functions. The GH3.17 subfamily harbored the highest number of the cis-regulatory elements, most having promoters towards dehydration-responsiveness. The RNA expression analysis revealed that 10 and 8 genes in drought and salinity stress conditions respectively were upregulated in G. hirsutum. All the genes that were upregulated in plants under salt stress conditions were also upregulated in drought stress; moreover, Gh_A08G1120 (GH3.5) exhibited a significant upregulation across the two stress factors. Functional characterization of Gh_A08G1120 (GH3.5) through virus-induced gene silencing (VIGS) revealed that the VIGS plants ability to tolerate drought and salt stresses was significantly reduced compared to the wild types. The chlorophyll content, relative leaf water content (RLWC), and superoxide dismutase (SOD) concentration level were reduced significantly while malondialdehyde concentration and ion leakage as a measure of cell membrane stability (CMS) increased in VIGS plants under drought and salt stress conditions.

CONCLUSION

This study revealed the significance of the GH3 genes in enabling the plant's adaptation to drought and salt stress conditions as evidenced by the VIGS results and RT-qPCR analysis.

Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition

Iron is a key transition element in the biosphere and is crucial for living organisms, although its cellular excess can be deleterious. Maintaining the balance of optimal iron availability in the model plant Arabidopsis (Arabidopsis thaliana) requires the precise operation of iron import through the principal iron transporter IRON-REGULATED TRANSPORTER1 (IRT1). Targeted inhibition of IRT1 can prevent oxidative stress, thus promoting plant survival. Here, we report the identification of an IRT1 inhibitor, namely the C2 domain-containing peripheral membrane protein ENHANCED BENDING1 (EHB1). EHB1 interacts with the cytoplasmically exposed variable region of IRT1, and we demonstrate that this interaction is greatly promoted by the presence of calcium. We found that EHB1 binds lipids characteristic of the plasma membrane, and the interaction between EHB1 and plant membranes is calcium-dependent. Molecular simulations showed that EHB1 membrane binding is a two-step process that precedes the interaction between EHB1 and IRT1. Genetic and physiological analyses indicated that EHB1 acts as a negative regulator of iron acquisition. The presence of EHB1 prevented the IRT1-mediated complementation of iron-deficient fet3fet4 yeast (Saccharomyces cerevisiae). Our data suggest that EHB1 acts as a direct inhibitor of IRT1-mediated iron import into the cell. These findings represent a major step in understanding plant iron acquisition, a process that underlies the primary production of bioavailable iron for land ecosystems.

Overexpression of S-nitrosoglutathione reductase alleviated iron-deficiency stress by regulating iron distribution and redox homeostasis

Iron (Fe) is an essential micronutrient element for plant growth. The S-nitrosoglutathione reductase (GSNOR) gene's functions under Fe-deficiency conditions are not well understood. Here, GSNOR expression was induced by Fe deficiency in tomato (Solanum lycopersicum L.) leaves and roots, while its overexpression alleviated chlorosis under Fe-deficiency conditions. GSNOR overexpression positively regulated the Fe distribution from root to shoot, which might result from the transcriptional regulation of genes involved in Fe metabolism. Additionally, the overexpression of GSNOR maintained redox homeostasis and protected chloroplasts from Fe-deficiency-related damage, resulting in a greater photosynthetic capacity. As a nitric oxide regulator, GSNOR's overexpression decreased the excessive accumulation of nitric oxide and S-nitrosothiols during the Fe deficiency, and maintained the homeostases of reactive oxygen species and reactive nitrogen species. Moreover, GSNOR overexpression, probably at the level of genes and proteins, along with protein S-nitrosylation, promoted Fe uptake and regulated the shoot/root Fe ratio under Fe-deficiency conditions.