GmVTL1a is an iron transporter on the symbiosome membrane of soybean with an important role in nitrogen fixation

Identification, characterization, and function analysis of the VIT family in Phaeodactylum tricornutum

Iron is an essential microelement for all living organisms. The vacuolar iron transporters (VIT) gene family is found in various species, including yeast, fungi, protozoa, and plants, where it plays a crucial role in sequestration, homeostasis, and tolerance of the heavy metals, particularly iron and manganese. However, the presence and function of VIT genes in marine phytoplankton have not been previously reported. The study aims to identify the VIT family within the marine diatom Phaeodactylum tricornutum and to analyze the function of these genes. We conducted a comprehensive analysis of the VIT genes in P. tricornutum genome, examining their phylogenetic relationship, physicochemical properties, gene structures, conserved motifs, domains, expression profile, and cis-acting elements using in silico methods. Function analysis were performed through complementation experiments and the expression of eGFP fusion protein in yeast. Four members of the VIT family were identified in P. tricornutum. All belonging to the VTL (VIT like) group in phylogenetic tree and containing a VIT1 domain. These genes are distributed across chromosomes 2, 4, and 13, with tandem duplication of the PtVTL1 and PtVTL2 contributed to the expansion of this gene family. Expression profile showed that the PtVTL3 is induced to express highly under light condition, others are induced to express highly under dark. PtVTL2 is highly induced to express at low Fe condition, and PtVTL3 is highly induced to express at high Fe condition. Analysis of cis-acting regulatory elements indicated that these genes are primarily involved in responses to environmental stress and phytohormones. Heterologous expression of PtVTL3 successfully rescued the iron-sensitive phenotype in yeast mutant △ccc1. The expression of eGFP-PtVTL3 fusion protein in yeast demonstrated that PtVTL3 is located to the tonoplast. These findings suggest that PtVTL3 function to transport Fe2+ across the tonoplast into the vacuole, thereby maintaining iron homeostasis in yeast. Four PtVTL genes were identified in the genome of P. tricornutum, with PtVTL3 playing a key role in iron transport at the tonoplast, highlighting its potential significance in iron homeostasis in marine diatoms.

Arabidopsis MEB3 functions as a vacuolar metal transporter to regulate iron accumulation in roots

Iron is an essential nutrient for plant photosynthesis and development, but excess iron leads to stress. After absorption from the soil, plants store iron in roots and distribute it to shoots via long-distance transport. The vacuole is involved in iron storage and the maintenance of cellular iron homeostasis, and vacuolar iron transporter (VIT) family proteins have been identified as plant vacuolar iron transporters. However, the contribution of vacuolar iron transporters to overall iron homeostasis in plants is not fully understood. Here, we show that MEMBRANE PROTEIN OF ER BODY 3 (MEB3), a VIT family member, functions as a vacuolar metal transporter for iron distribution in Arabidopsis thaliana. Heterologous expression of Arabidopsis MEB3 in yeast vacuolar iron or zinc transporter mutants restored the iron- and zinc-resistance phenotypes of the respective mutants, indicating that MEB3 regulates iron and zinc transport. In Arabidopsis, MEB3 was expressed in almost all tissues, albeit to higher levels in roots and seedlings, and MEB3 protein localized to the tonoplast. Iron but not zinc levels were reduced in meb3 knockout mutant roots, suggesting that the knockout reduced iron storage capacity in roots. At high iron concentration, meb3 mutants accumulated more iron in shoots and less iron in roots than the wild type, indicating impairment of proper iron distribution in meb3 mutants. These findings demonstrate that MEB3 is a vacuolar transporter involved in the homeostasis of iron and other metals in plants.

The Rhizophagus irregularis permease RiFTR1 functions without a ferroxidase partner for reductive iron transport

The contribution of arbuscular mycorrhizal fungi (AM fungi) to plant iron (Fe) acquisition has been demonstrated in several studies. A previous investigation revealed that the AM fungus Rhizophagus irregularis utilizes a high-affinity reductive pathway for Fe uptake, mediated by the Fe transporter RiFTR1. In this study, we used a genome-wide approach in R. irregularis to find genes encoding ferroxidases of the multicopper oxidase (MCO) gene family in an attempt to identify the ferroxidase partner of RiFTR1. Nine genes putatively encoding MCOs (RiMCO1-9) were identified. Yeast complementation assays demonstrated that RiMCO1 and RiMCO3 can function as ferroxidases, suggesting their involvement in the reductive Fe uptake pathway. Surprisingly, RiFTR1 was capable of transporting Fe in yeast without a ferroxidase partner, resembling the Fe transport mechanism of plant IRT1-like systems. RiFTR1 exhibited increase expression in arbuscules. Overexpression of RiFTR1 in Medicago truncatula roots led to enhanced mycorrhizal colonization and arbuscule abundance, highlighting the significance of Fe for AM symbiosis.

Understanding the Crucial Role of Phosphate and Iron Availability in Regulating Root Nodule Symbiosis

The symbiosis between legumes and nitrogen-fixing bacteria (rhizobia) is instrumental in sustaining the nitrogen cycle and providing fixed nitrogen to the food chain. Both partners must maintain an efficient nutrient exchange to ensure a successful symbiosis. This mini-review highlights the intricate phosphate and iron uptake and homeostasis processes taking place in legumes during their interactions with rhizobia. The coordination of transport and homeostasis of these nutrients in host plants and rhizobia ensures an efficient nitrogen fixation process and nutrient use. We discuss the genetic machinery controlling the uptake and homeostasis of these nutrients in the absence of rhizobia and under symbiotic conditions with this soil bacterium. We also highlight the genetic impact of the availability of phosphate and iron to coordinate the activation of the genetic programs that allow legumes to engage in symbiosis with rhizobia. Finally, we discuss how the transcription factor phosphate starvation response might be a crucial genetic element to integrate the plant's needs of nitrogen, iron and phosphate while interacting with rhizobia. Understanding the coordination of the iron and phosphate uptake and homeostasis can lead us to better harness the ecological benefits of the legume-rhizobia symbiosis, even under adverse environmental conditions.

Comparative impact analysis of nitrate reduction by typical components of natural organic compounds in magnetite-bearing riparian zones

As the key interface, the nitrate removal capacity of riparian zones is receiving close attention. Although naturally occurring organic compounds in this environment play a pivotal role in shaping microbial communities and influencing the nitrate removal capacity, the relevant research is inadequate. Given the complexity of riparian environments, in this study, we added representative natural organic matter (fulvic acid, butyric acid, naphthalene, starch, and sodium bicarbonate) as carbon conditions and incorporated magnetite to simulate riparian zone components. The study investigated the nitrate degradation efficiency and microbial responses under different natural carbon conditions in real iron-containing environments. Butyric acid exhibited the most efficient nitrate reduction, followed in descending order by naphthalene, starch, sodium bicarbonate, and humic acid. However, this did not imply that butyric acid efficiently removed nitrogen; instead, the nitrogen would circulate in the environment in the form of ammonium. Denitrification and DNRA were the primary drivers of nitrate reduction in each system, while naphthalene and humic acid systems also exhibited nitrification and mineralization. Nitrogen-fixing bacteria represent a unique microbial community in the butyrate system. Further, the synergistic degradation of naphthalene and nitrate demonstrated significant potential applications. High-throughput sequencing revealed that carbon conditions exerted selective pressure on microorganisms, driving Fe (Ⅱ)/Fe (Ⅲ) transformation by shaping the microbial community structure and influencing the nitrogen cycling process.

Inorganic nitrogen inhibits symbiotic nitrogen fixation through blocking NRAMP2-mediated iron delivery in soybean nodules

Symbiotic nitrogen fixation (SNF) in legume-rhizobia serves as a sustainable source of nitrogen (N) in agriculture. However, the addition of inorganic N fertilizers significantly inhibits SNF, and the underlying mechanisms remain not-well understood. Here, we report that inorganic N disrupts iron (Fe) homeostasis in soybean nodules, leading to a decrease in SNF efficiency. This disruption is attributed to the inhibition of the Fe transporter genes Natural Resistance-Associated Macrophage Protein 2a and 2b (GmNRAMP2a&2b) by inorganic N. GmNRAMP2a&2b are predominantly localized at the tonoplast of uninfected nodule tissues, affecting Fe transfer to infected cells and consequently, modulating SNF efficiency. In addition, we identified a pair of N-signal regulators, nitrogen-regulated GARP-type transcription factors 1a and 1b (GmNIGT1a&1b), that negatively regulate the expression of GmNRAMP2a&2b, which establishes a link between N signaling and Fe homeostasis in nodules. Our findings reveal a plausible mechanism by which soybean adjusts SNF efficiency through Fe allocation in response to fluctuating inorganic N conditions, offering valuable insights for optimizing N and Fe management in legume-based agricultural systems.

Insights into the ameliorative effect of ZnONPs on arsenic toxicity in soybean mediated by hormonal regulation, transporter modulation, and stress responsive genes

Arsenic (As) contamination of agricultural soils poses a serious threat to crop productivity and food safety. Zinc oxide nanoparticles (ZnONPs) have emerged as a potential amendment for mitigating the adverse effects of As stress in plants. Soybean crop is mostly grown on marginalized land and is known for high accumulation of As in roots than others tissue. Therefore, this study aimed to elucidate the underlying mechanisms of ZnONPs in ameliorating arsenic toxicity in soybean. Our results demonstrated that ZnOB significantly improved the growth performance of soybean plants exposed to arsenic. This improvement was accompanied by a decrease (55%) in As accumulation and an increase in photosynthetic efficiency. ZnOB also modulated hormonal balance, with a significant increase in auxin (149%), abscisic acid (118%), gibberellin (160%) and jasmonic acid content (92%) under As(V) stress assuring that ZnONPs may enhance root growth and development by regulating hormonal signaling. We then conducted a transcriptomic analysis to understand further the molecular mechanisms underlying the NPs-induced As(V) tolerance. This analysis identified genes differentially expressed in response to ZnONPs supplementation, including those involved in auxin, abscisic acid, gibberellin, and jasmonic acid biosynthesis and signaling pathways. Weighted gene co-expression network analysis identified 37 potential hub genes encoding stress responders, transporters, and signal transducers across six modules potentially facilitated the efflux of arsenic from cells, reducing its toxicity. Our study provides valuable insights into the molecular mechanisms associated with metalloid tolerance in soybean and offers new avenues for improving As tolerance in contaminated soils.

Driving mechanism of different nutrient conditions on microbial mediated nitrate reduction in magnetite-present river infiltration zone

Significant research is focused on the ability of riparian zones to reduce groundwater nitrate contamination. Owing to the extremely high redox activity of nitrate, naturally existing electron donors, such as organic matter and iron minerals, are crucial in facilitating nitrate reduction in the riparian zone. Here, we examined the coexistence of magnetite, an iron mineral, and nitrate, a frequently observed coexisting system in sediments, to investigate nitrate reduction features at various C/N ratios and evaluate the response of microbial communities to these settings. Additionally, we aimed to use this information as a foundation for examining the effect of nutritional conditions on the nitrate reduction process in magnetite-present environments. These results emphasise the significance of organic matter in enabling dissimilatory nitrate reduction to ammonium (DNRA) and enhancing the connection between nitrate reduction and iron in sedimentary environments. In the later phases of nitrate reduction, nitrogen fixation was the prevailing process in low-carbon environments, whereas high-carbon environments tended to facilitate the breakdown of organic nitrogen. High-throughput sequencing analysis revealed a robust association between C/N ratios and alterations in microbial community composition, providing insights into notable modifications in essential functioning microorganisms. The nitrogen-fixing bacterium Ralstonia is more abundant in ecosystems with scarce organic matter. In contrast, in settings rich in organic matter, microorganisms, such as Acinetobacter and Clostridia, which may produce ammonia, play crucial roles. Moreover, the population of iron bacteria grows in such an environment. Hence, this study proposes that C/N ratios can influence Fe(II)/Fe(III) conversions and simultaneously affect the process of nitrate reduction by shaping the composition of specific microbial communities.

Metal nutrition and transport in the process of symbiotic nitrogen fixation

Symbiotic nitrogen fixation (SNF) facilitated by the interaction between legumes and rhizobia is a well-documented and eco-friendly alternative to chemical nitrogen fertilizers. Host plants obtain fixed nitrogen from rhizobia by providing carbon and mineral nutrients. These mineral nutrients, which are mostly in the form of metal ions, are implicated in various stages of the SNF process. This review describes the functional roles played by metal ions in nodule formation and nitrogen fixation and specifically addresses their transport mechanisms and associated transporters within root nodules. Future research directions and potential strategies for enhancing SNF efficiency are also discussed.

γ-Aminobutyric acid (GABA) in N2-fixing-legume symbiosis: Metabolic flux and carbon/nitrogen homeostasis in responses to abiotic constraints

Nodule symbiosis is an energetic process that demands a tremendous carbon (C) cost, which massively increases in responses to environmental stresses. Notably, most common respiratory pathways (e.g., glycolysis and Krebs cycle) that sustain nitrogenase activity and subsequent nitrogen (N) assimilation (amino acid formation) display a noncyclic mode of C flux. In such circumstances, the nodule's energy charge could markedly decrease, leading to a lower symbiotic activity under stresses. The host plant then attempts to induce alternative robust metabolic pathways to minimize the C expenditure and compensate for the loss in respiratory substrates. GABA (γ-aminobutyric acid) shunt appears to be among the highly conserved metabolic bypass induced in responses to stresses. Thus, it can be suggested that GABA, via its primary biosynthetic pathway (GABA shunt), is simultaneously induced to circumvent stress-susceptible decarboxylating portion of the Krebs cycle and to replenish symbiosome with energy and C skeletons for enhancing nitrogenase activity and N assimilation besides the additional C costs expended in the metabolic stress acclimations (e.g., biosynthesis of secondary metabolites and excretion of anions). The GABA-mediated C/N balance is strongly associated with interrelated processes, including pH regulation, oxygen (O2) protection, osmoregulation, cellular redox control, and N storage. Furthermore, it has been anticipated that GABA could be implicated in other functions beyond its metabolic role (i.e., signaling and transport). GABA helps plants possess remarkable metabolic plasticity, which might thus assist nodules in attenuating stressful events.

IMA peptides regulate root nodulation and nitrogen homeostasis by providing iron according to internal nitrogen status

Legumes control root nodule symbiosis (RNS) in response to environmental nitrogen availability. Despite the recent understanding of the molecular basis of external nitrate-mediated control of RNS, it remains mostly elusive how plants regulate physiological processes depending on internal nitrogen status. In addition, iron (Fe) acts as an essential element that enables symbiotic nitrogen fixation; however, the mechanism of Fe accumulation in nodules is poorly understood. Here, we focus on the transcriptome in response to internal nitrogen status during RNS in Lotus japonicus and identify that IRON MAN (IMA) peptide genes are expressed during symbiotic nitrogen fixation. We show that LjIMA1 and LjIMA2 expressed in the shoot and root play systemic and local roles in concentrating internal Fe to the nodule. Furthermore, IMA peptides have conserved roles in regulating nitrogen homeostasis by adjusting nitrogen-Fe balance in L. japonicus and Arabidopsis thaliana. These findings indicate that IMA-mediated Fe provision plays an essential role in regulating nitrogen-related physiological processes.

Expression and mutagenesis studies in the Medicago truncatula iron transporter MtVTL8 confirm its role in symbiotic nitrogen fixation and reveal amino acids essential for transport

The model legume Medicago truncatula establishes a symbiosis with soil bacteria (rhizobia) that carry out symbiotic nitrogen fixation (SNF) in plant root nodules. SNF requires the exchange of nutrients between the plant and rhizobia in the nodule that occurs across a plant-derived symbiosome membrane. One iron transporter, belonging to the Vacuolar iron Transporter-Like (VTL) family, MtVTL8, has been identified as essential for bacteria survival and therefore SNF. In this work we investigated the spatial expression of MtVTL8 in nodules and addressed whether it could be functionally interchangeable with a similar nodule-expressed iron transporter, MtVTL4. Using a structural model for MtVTL8 and the previously hypothesized mechanism for iron transport in a phylogenetically-related Vacuolar Iron Transporter (VIT), EgVIT1 with known crystal structure, we identified critical amino acids and obtained their mutants. Mutants were tested in planta for complementation of an SNF defective line and in an iron sensitive mutant yeast strain. An extended phylogenetic assessment of VTLs and VITs showed that amino acids critical for function are conserved differently in VTLs vs. VITs. Our studies showed that some amino acids are essential for iron transport leading us to suggest a model for MtVTL8 function, one that is different for other iron transporters (VITs) studied so far. This study extends the understanding of iron transport mechanisms in VTLs as well as those used in SNF.

Agrobacterium rhizogenes: paving the road to research and breeding for woody plants

Woody plants play a vital role in global ecosystems and serve as valuable resources for various industries and human needs. While many woody plant genomes have been fully sequenced, gene function research and biotechnological breeding advances have lagged behind. As a result, only a limited number of genes have been elucidated, making it difficult to use newer tools such as CRISPR-Cas9 for biotechnological breeding purposes. The use of Agrobacterium rhizogenes as a transformative tool in plant biotechnology has received considerable attention in recent years, particularly in the research field on woody plants. Over the past three decades, numerous woody plants have been effectively transformed using A. rhizogenes-mediated techniques. Some of these transformed plants have successfully regenerated. Recent research on A. rhizogenes-mediated transformation of woody plants has demonstrated its potential for various applications, including gene function analysis, gene expression profiling, gene interaction studies, and gene regulation analysis. The introduction of the Ri plasmid has resulted in the emergence of several Ri phenotypes, such as compact plant types, which can be exploited for Ri breeding purposes. This review paper presents recent advances in A. rhizogenes-mediated basic research and Ri breeding in woody plants. This study highlights various aspects of A. rhizogenes-mediated transformation, its multiple applications in gene function analysis, and the potential of Ri lines as valuable breeding materials.

Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains

BACKGROUND

Symbiotic nitrogen fixation differs among Bradyrhizobium japonicum strains. Soybean inoculated with USDA123 has a lower yield than strains known to have high nitrogen fixation efficiency, such as USDA110. In the main soybean-producing area in the Midwest of the United States, USDA123 has a high nodule incidence in field-grown soybean and is competitive but inefficient in nitrogen fixation. In this study, a high-throughput system was developed to characterize nodule number among 1,321 Glycine max and 69 Glycine soja accessions single inoculated with USDA110 and USDA123.

RESULTS

Seventy-three G. max accessions with significantly different nodule number of USDA110 and USDA123 were identified. After double inoculating 35 of the 73 accessions, it was observed that PI189939, PI317335, PI324187B, PI548461, PI562373, and PI628961 were occupied by USDA110 and double-strain nodules but not by USDA123 nodules alone. PI567624 was only occupied by USDA110 nodules, and PI507429 restricted all strains. Analysis showed that 35 loci were associated with nodule number in G. max when inoculated with strain USDA110 and 35 loci with USDA123. Twenty-three loci were identified in G. soja when inoculated with strain USDA110 and 34 with USDA123. Only four loci were common across two treatments, and each locus could only explain 0.8 to 1.5% of phenotypic variation.

CONCLUSIONS

High-throughput phenotyping systems to characterize nodule number and occupancy were developed, and soybean germplasm restricting rhizobium strain USDA123 but preferring USDA110 was identified. The larger number of minor effects and a small few common loci controlling the nodule number indicated trait genetic complexity and strain-dependent nodulation restriction. The information from the present study will add to the development of cultivars that limit USDA123, thereby increasing nitrogen fixation efficiency and productivity.

Forging a symbiosis: transition metal delivery in symbiotic nitrogen fixation

Symbiotic nitrogen fixation carried out by the interaction between legumes and rhizobia is the main source of nitrogen in natural ecosystems and in sustainable agriculture. For the symbiosis to be viable, nutrient exchange between the partners is essential. Transition metals are among the nutrients delivered to the nitrogen-fixing bacteria within the legume root nodule cells. These elements are used as cofactors for many of the enzymes controlling nodule development and function, including nitrogenase, the only known enzyme able to convert N2 into NH3 . In this review, we discuss the current knowledge on how iron, zinc, copper, and molybdenum reach the nodules, how they are delivered to nodule cells, and how they are transferred to nitrogen-fixing bacteria within.

Iron in the Symbiosis of Plants and Microorganisms

Iron is an essential element for most organisms. Both plants and microorganisms have developed different mechanisms for iron uptake, transport and storage. In the symbiosis systems, such as rhizobia-legume symbiosis and arbuscular mycorrhizal (AM) symbiosis, maintaining iron homeostasis to meet the requirements for the interaction between the host plants and the symbiotic microbes is a new challenge. This intriguing topic has drawn the attention of many botanists and microbiologists, and many discoveries have been achieved so far. In this review, we discuss the current progress on iron uptake and transport in the nodules and iron homeostasis in rhizobia-legume symbiosis. The discoveries with regard to iron uptake in AM fungi, iron uptake regulation in AM plants and interactions between iron and other nutrient elements during AM symbiosis are also summarized. At the end of this review, we propose prospects for future studies in this fascinating research area.

Rapid Changes to Endomembrane System of Infected Root Nodule Cells to Adapt to Unusual Lifestyle

Symbiosis between leguminous plants and soil bacteria rhizobia is a refined type of plant-microbial interaction that has a great importance to the global balance of nitrogen. The reduction of atmospheric nitrogen takes place in infected cells of a root nodule that serves as a temporary shelter for thousands of living bacteria, which, per se, is an unusual state of a eukaryotic cell. One of the most striking features of an infected cell is the drastic changes in the endomembrane system that occur after the entrance of bacteria to the host cell symplast. Mechanisms for maintaining intracellular bacterial colony represent an important part of symbiosis that have still not been sufficiently clarified. This review focuses on the changes that occur in an endomembrane system of infected cells and on the putative mechanisms of infected cell adaptation to its unusual lifestyle.

Combination of Hairy Root and Whole-Plant Transformation Protocols to Achieve Efficient CRISPR/Cas9 Genome Editing in Soybean

The new gene-editing technology CRISPR/Cas system has been widely used for genome engineering in various organisms. Since the CRISPR/Cas gene-editing system has a certain possibility of low efficiency and the whole plant transformation of soybean is time-consuming and laborious, it is important to evaluate the editing efficiency of designed CRISPR constructs before the stable whole plant transformation process starts. Here, we provide a modified protocol for generating transgenic hairy soybean roots to assess the efficiency of guide RNA (gRNA) sequences of the CRISPR/Cas constructs within 14 days. The cost- and space-effective protocol was first tested in transgenic soybean harboring the GUS reporter gene for the efficiency of different gRNA sequences. Targeted DNA mutations were detected in 71.43-97.62% of the transgenic hairy roots analyzed as evident by GUS staining and DNA sequencing of the target region. Among the four designed gene-editing sites, the highest editing efficiency occurred at the 3' terminal of the GUS gene. In addition to the reporter gene, the protocol was tested for the gene-editing of 26 soybean genes. Among the gRNAs selected for stable transformation, the editing efficiency of hairy root transformation and stable transformation ranged from 5% to 88.8% and 2.7% to 80%, respectively. The editing efficiencies of stable transformation were positively correlated with those of hairy root transformation with a Pearson correlation coefficient (r) of 0.83. Our results demonstrated that soybean hairy root transformation could rapidly assess the efficiency of designed gRNA sequences on genome editing. This method can not only be directly applied to the functional study of root-specific genes, but more importantly, it can be applied to the pre-screening of gRNA in CRISPR/Cas gene editing.

Quantitative proteomics reveals key pathways in the symbiotic interface and the likely extracellular property of soybean symbiosome

An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plant-rhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation. Here, we report a comprehensive proteome atlas of the soybean symbiosome membrane (SM), peribacteroid space (PBS), and root microsomal fraction (RMF) using state-of-the-art label-free quantitative proteomic technology. In total, 1759 soybean proteins with diverse functions are detected in the SM, and 1476 soybean proteins and 369 rhizobial proteins are detected in the PBS. The diversity of SM proteins detected suggests multiple origins of the SM. Quantitative comparative analysis highlights amino acid metabolism and nutrient uptake in the SM, indicative of the key pathways in nitrogen assimilation. The detection of soybean secretory proteins in the PBS and receptor-like kinases in the SM provides evidence for the likely extracellular property of the symbiosome and the potential signaling communication between both symbionts at the symbiotic interface. Our proteomic data provide clues for how some of the sophisticated regulation between soybean and rhizobium at the symbiotic interface is achieved, and suggest approaches for symbiosis engineering.

GmYSL7 controls iron uptake, allocation, and cellular response of nodules in soybean

Iron (Fe) is essential for DNA synthesis, photosynthesis and respiration of plants. The demand for Fe substantially increases during legumes-rhizobia symbiotic nitrogen fixation because of the synthesis of leghemoglobin in the host and Fe-containing proteins in bacteroids. However, the mechanism by which plant controls iron transport to nodules remains largely unknown. Here we demonstrate that GmYSL7 serves as a key regulator controlling Fe uptake from root to nodule and distribution in soybean nodules. GmYSL7 is Fe responsive and GmYSL7 transports iron across the membrane and into the infected cells of nodules. Alterations of GmYSL7 substantially affect iron distribution between root and nodule, resulting in defective growth of nodules and reduced nitrogenase activity. GmYSL7 knockout increases the expression of GmbHLH300, a transcription factor required for Fe response of nodules. Overexpression of GmbHLH300 decreases nodule number, nitrogenase activity and Fe content in nodules. Remarkably, GmbHLH300 directly binds to the promoters of ENOD93 and GmLbs, which regulate nodule number and nitrogenase activity, and represses their transcription. Our data reveal a new role of GmYSL7 in controlling Fe transport from host root to nodule and Fe distribution in nodule cells, and uncover a molecular mechanism by which Fe affects nodule number and nitrogenase activity.

Innovation and appropriation in mycorrhizal and rhizobial Symbioses

Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.

Micronutrient homeostasis in plants for more sustainable agriculture and healthier human nutrition

The provision of sustainable, sufficient, and nutritious food to the growing population is a major challenge for agriculture and the plant research community. In this respect, the mineral micronutrient content of food crops deserves particular attention. Micronutrient deficiencies in cultivated soils and plants are a global problem that adversely affects crop production and plant nutritional value, as well as human health and well-being. In this review, we call for awareness of the importance and relevance of micronutrients in crop production and quality. We stress the need for better micronutrient nutrition in human populations, not only in developing but also in developed nations, and describe strategies to identify and characterize new varieties with high micronutrient content. Furthermore, we explain how adequate nutrition of plants with micronutrients impacts metabolic functions and the capacity of plants to express tolerance mechanisms against abiotic and biotic constraints. Finally, we provide a brief overview and a critical discussion on current knowledge, future challenges, and specific technological needs for research on plant micronutrient homeostasis. Research in this area is expected to foster the sustainable development of nutritious and healthy food crops for human consumption.

Posttranslational regulation of transporters important for symbiotic interactions

Coordinated sharing of nutritional resources is a central feature of symbiotic interactions, and, despite the importance of this topic, many questions remain concerning the identification, activity, and regulation of transporter proteins involved. Recent progress in obtaining genome and transcriptome sequences for symbiotic organisms provides a wealth of information on plant, fungal, and bacterial transporters that can be applied to these questions. In this update, we focus on legume-rhizobia and mycorrhizal symbioses and how transporters at the symbiotic interfaces can be regulated at the protein level. We point out areas where more research is needed and ways that an understanding of transporter mechanism and energetics can focus hypotheses. Protein phosphorylation is a predominant mechanism of posttranslational regulation of transporters in general and at the symbiotic interface specifically. Other mechanisms of transporter regulation, such as protein-protein interaction, including transporter multimerization, polar localization, and regulation by pH and membrane potential are also important at the symbiotic interface. Most of the transporters that function in the symbiotic interface are members of transporter families; we bring in relevant information on posttranslational regulation within transporter families to help generate hypotheses for transporter regulation at the symbiotic interface.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

A roadmap of plant membrane transporters in arbuscular mycorrhizal and legume-rhizobium symbioses

Most land plants live in close contact with beneficial soil microbes: the majority of land plant species establish symbiosis with arbuscular mycorrhizal fungi, while most legumes, the third largest plant family, can form a symbiosis with nitrogen-fixing rhizobia. These microbes contribute to plant nutrition via endosymbiotic processes that require modulating the expression and function of plant transporter systems. The efficient contribution of these symbionts involves precisely controlled integration of transport, which is enabled by the adaptability and plasticity of their transporters. Advances in our understanding of these systems, driven by functional genomics research, are rapidly filling the gap in knowledge about plant membrane transport involved in these plant-microbe interactions. In this review, we synthesize recent findings associated with different stages of these symbioses, from the pre-symbiotic stage to nutrient exchange, and describe the role of host transport systems in both mycorrhizal and legume-rhizobia symbioses.

Soybean Yellow Stripe-like 7 is a symbiosome membrane peptide transporter important for nitrogen fixation

Legumes form a symbiosis with rhizobia that convert atmospheric nitrogen (N2) to ammonia and provide it to the plant in return for a carbon and nutrient supply. Nodules, developed as part of the symbiosis, harbor rhizobia that are enclosed in a plant-derived symbiosome membrane (SM) to form an organelle-like structure called the symbiosome. In mature nodules exchanges between the symbionts occur across the SM. Here we characterize Yellow Stripe-like 7 (GmYSL7), a Yellow stripe-like family member localized on the SM in soybean (Glycine max) nodules. It is expressed specifically in infected cells with expression peaking soon after nitrogenase becomes active. Unlike most YSL family members, GmYSL7 does not transport metals complexed with phytosiderophores. Rather, it transports oligopeptides of between four and 12 amino acids. Silencing GmYSL7 reduces nitrogenase activity and blocks infected cell development so that symbiosomes contain only a single bacteroid. This indicates the substrate of YSL7 is required for proper nodule development, either by promoting symbiosome development directly or by preventing inhibition of development by the plant. RNAseq of nodules where GmYSL7 was silenced suggests that the plant initiates a defense response against rhizobia with genes encoding proteins involved in amino acid export downregulated and some transcripts associated with metal homeostasis altered. These changes may result from the decrease in nitrogen fixation upon GmYSL7 silencing and suggest that the peptide(s) transported by GmYSL7 monitor the functional state of the bacteroids and regulate nodule metabolism and transport processes accordingly. Further work to identify the physiological substrate for GmYSL7 will allow clarification of this role.

Role of a vacuolar iron transporter OsVIT2 in the distribution of iron to rice grains

Iron (Fe) from rice grains is an important source of dietary intake; however, the molecular mechanisms responsible for loading of Fe to the grains are poorly understood. We functionally characterized a vacuolar iron transporter gene, OsVIT2 in terms of expression pattern, cellular localization, and mutant phenotypes. OsVIT2 was expressed in the parenchyma cell bridges of nodes, in the mestome sheath of leaf sheath and aleurone of the caryopsis. Mutation of OsVIT2 resulted in decreased Fe distribution to the leaf sheath, nodes, and aleurone, but increased Fe to the leaf blade and grains. Furthermore, Fe was heavily deposited in the parenchyma cell bridges, mestome sheath and aleurone in the wild-type rice, but this accumulation was decreased in the knockout lines. Conversely, heavier deposition of Fe was observed in the embryo and endosperm of the grains of knockout lines compared with the wild-type rice, resulting in increased Fe accumulation in the polished rice without yield penalty. These results indicate that OsVIT2 is involved in the distribution of Fe to the grains through sequestering Fe into vacuoles in mestome sheath, nodes, and aleurone layer and that knockout of this gene provides a potential way for Fe biofortification without yield penalty.

The R2R3-MYB transcription factor MtMYB134 orchestrates flavonol biosynthesis in Medicago truncatula

Our results provide insights into the flavonol biosynthesis regulation of M. truncatula. The R2R3-MYB transcription factor MtMYB134 emerged as tool to improve the flavonol biosynthesis. Flavonols are plant specialized metabolites with vital roles in plant development and defense and are known as diet compound beneficial to human health. In leguminous plants, the regulatory proteins involved in flavonol biosynthesis are not well characterized. Using a homology-based approach, three R2R3-MYB transcription factor encoding genes have been identified in the Medicago truncatula reference genome sequence. The gene encoding a protein with highest similarity to known flavonol regulators, MtMYB134, was chosen for further experiments and was characterized as a functional flavonol regulator from M. truncatula. MtMYB134 expression levels are correlated with the expression of MtFLS2, encoding a key enzyme of flavonol biosynthesis, and with flavonol metabolite content. MtMYB134 was shown to activate the promoters of the A. thaliana flavonol biosynthesis genes AtCHS and AtFLS1 in Arabidopsis protoplasts in a transactivation assay and to interact with the Medicago promoters of MtCHS2 and MtFLS2 in yeast 1-hybrid assays. To ascertain the functional aspect of the identified transcription factor, we developed a sextuple mutant, which is defective in anthocyanin and flavonol biosynthesis. Ectopic expression of MtMYB134 in a multiple myb A. thaliana mutant restored flavonol biosynthesis. Furthermore, overexpression of MtMYB134 in hairy roots of M. truncatula enhanced the biosynthesis of various flavonol derivatives. Taken together, our results provide insight into the understanding of flavonol biosynthesis regulation in M. truncatula and provides MtMYB134 as tool for genetic manipulation to improve flavonol synthesis.

Vacuolar Iron Transporter (Like) proteins: Regulators of cellular iron accumulation in plants

Iron is not only important for plant physiology, but also a very important micronutrient in human diets. The vacuole is the main site for accumulation of excess amounts of various nutrients and toxic substances in plant cells. During the past decade, many Vacuolar Iron Transporter (VIT) and VIT-Like (VTL) genes have been identified and shown to play important roles in iron homeostasis in different plants. Furthermore, recent reports identified novel roles of these transporter genes in symbiotic nitrogen fixation (SNF) in legume crops as well as in the blue coloration of petals in flowers. The literature indicates their universal role in Fe transport across different tissues (grains, nodules, flowers) to different biological processes (cellular iron homeostasis, SNF, petal coloration) in different plants. Here, we have systematically reviewed different aspects, such as structure, molecular evolution, expression, and function of VIT/VTL proteins. This will help future studies aimed at functional analysis of VIT/VTL genes in other plant species, vacuolar transportation mechanisms, and iron biofortification at large.

The cross-kingdom roles of mineral nutrient transporters in plant-microbe relations

The regulation of plant physiology by plant mineral nutrient transporter (MNT) is well understood. Recently, the extensive characterization of beneficial and pathogenic plant-microbe interactions has defined the roles for MNTs in such relationships. In this review, we summarize the roles of diverse nutrient transporters in the symbiotic or pathogenic relationships between plants and microorganisms. In doing so, we highlight how MNTs of plants and microbes can act in a coordinated manner. In symbiotic relationships, MNTs play key roles in the establishment of the interaction between the host plant and rhizobium or mycorrhizae as well in the subsequent coordinated transport of nutrients. Additionally, MNTs may also regulate the colonization or degeneration of symbiotic microorganisms by reflecting the nutrient status of the plant and soil. This allows the host plant obtain nutrients from the soil in the most optimal manner. With pathogenic-interactions, MNTs influence pathogen proliferation, the efficacy of the host's biochemical defense and related signal transduction mechanisms. We classify the MNT effects in plant-pathogen interactions as either indirect by influencing the nutrient status and fitness of the pathogen, or direct by initiating host defense mechanisms. While such observations indicate the fundamental importance of MNTs in governing the interactions with a range of microorganisms, further work is needed to develop an integrative understanding of their functions.

Iron Transport across Symbiotic Membranes of Nitrogen-Fixing Legumes

Iron is an essential nutrient for the legume-rhizobia symbiosis and nitrogen-fixing bacteroids within root nodules of legumes have a very high demand for the metal. Within the infected cells of nodules, the bacteroids are surrounded by a plant membrane to form an organelle-like structure called the symbiosome. In this review, we focus on how iron is transported across the symbiosome membrane and accessed by the bacteroids.

The Medicago truncatula Yellow Stripe1-Like3 gene is involved in vascular delivery of transition metals to root nodules

Symbiotic nitrogen fixation carried out in legume root nodules requires transition metals. These nutrients are delivered by the host plant to the endosymbiotic nitrogen-fixing bacteria living within the nodule cells, a process in which vascular transport is essential. As members of the Yellow Stripe-Like (YSL) family of metal transporters are involved in root to shoot transport, they should also be required for root to nodule metal delivery. The genome of the model legume Medicago truncatula encodes eight YSL proteins, four of them with a high degree of similarity to Arabidopsis thaliana YSLs involved in long-distance metal trafficking. Among them, MtYSL3 is a plasma membrane protein expressed by vascular cells in roots and nodules and by cortical nodule cells. Reducing the expression level of this gene had no major effect on plant physiology when assimilable nitrogen was provided in the nutrient solution. However, nodule functioning was severely impaired, with a significant reduction of nitrogen fixation capabilities. Further, iron and zinc accumulation and distribution changed. Iron was retained in the apical region of the nodule, while zinc became strongly accumulated in the nodule veins in the ysl3 mutant. These data suggest a role for MtYSL3 in vascular delivery of iron and zinc to symbiotic nitrogen fixation.

Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi

Iron is an essential micronutrient for most living beings since it participates as a redox active cofactor in many biological processes including cellular respiration, lipid biosynthesis, DNA replication and repair, and ribosome biogenesis and recycling. However, when present in excess, iron can participate in Fenton reactions and generate reactive oxygen species that damage cells at the level of proteins, lipids and nucleic acids. Organisms have developed different molecular strategies to protect themselves against the harmful effects of high concentrations of iron. In the case of fungi and plants, detoxification mainly occurs by importing cytosolic iron into the vacuole through the Ccc1/VIT1 iron transporter. New sequenced genomes and bioinformatic tools are facilitating the functional characterization, evolution and ecological relevance of metabolic pathways and homeostatic networks across the Tree of Life. Sequence analysis shows that Ccc1/VIT1 homologs are widely distributed among organisms with the exception of animals. The recent elucidation of the crystal structure of a Ccc1/VIT1 plant ortholog has enabled the identification of both conserved and species-specific motifs required for its metal transport mechanism. Moreover, recent studies in the yeast Saccharomyces cerevisiae have also revealed that multiple transcription factors including Yap5 and Msn2/Msn4 contribute to the expression of CCC1 in high-iron conditions. Interestingly, Malaysian S. cerevisiae strains express a partially functional Ccc1 protein that renders them sensitive to iron. Different regulatory mechanisms have been described for non-Saccharomycetaceae Ccc1 homologs. The characterization of Ccc1/VIT1 proteins is of high interest in the development of biofortified crops and the protection against microbial-derived diseases.

The Medicago truncatula Vacuolar iron Transporter-Like proteins VTL4 and VTL8 deliver iron to symbiotic bacteria at different stages of the infection process

The symbiotic relationship between legumes and rhizobium bacteria in root nodules has a high demand for iron, and questions remain regarding which transporters are involved. Here, we characterize two nodule-specific Vacuolar iron Transporter-Like (VTL) proteins in Medicago truncatula. Localization of fluorescent fusion proteins and mutant studies were carried out to correlate with existing RNA-seq data showing differential expression of VTL4 and VTL8 during early and late infection, respectively. The vtl4 insertion lines showed decreased nitrogen fixation capacity associated with more immature nodules and less elongated bacteroids. A mutant line lacking the tandemly-arranged VTL4-VTL8 genes, named 13U, was unable to develop functional nodules and failed to fix nitrogen, which was almost fully restored by expression of VTL8 alone. Using a newly developed lux reporter to monitor iron status of the bacteroids, a moderate decrease in luminescence signal was observed in vtl4 mutant nodules and a strong decrease in 13U nodules. Iron transport capability of VTL4 and VTL8 was shown by yeast complementation. These data indicate that VTL8, the closest homologue of SEN1 in Lotus japonicus, is the main route for delivering iron to symbiotic rhizobia. We propose that a failure in iron protein maturation leads to early senescence of the bacteroids.