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Nitrogen (N) and carbon (C) are essential elements for plant growth and crop yield. Thus, improved N and C utilisation contributes to agricultural productivity and reduces the need for fertilisation. In the present study, we find that overexpression of a single rice gene, Oryza sativa plasma membrane (PM) H + -ATPase 1 ( OSA1 ), facilitates ammonium absorption and assimilation in roots and enhanced light-induced stomatal opening with higher photosynthesis rate in leaves. As a result, OSA1 overexpression in rice plants causes a 33% increase in grain yield and a 46% increase in N use efficiency overall. As PM H + -ATPase is highly conserved in plants, these findings indicate that the manipulation of PM H + -ATPase could cooperatively improve N and C utilisation, potentially providing a vital tool for food security and sustainable agriculture. Improved utilisation of nitrogen and carbon could boost agricultural productivity. Here Zhang et al. show that overexpression of a single gene, encoding the plasma membrane H +  -ATPase 1 OSA1, is able to increase both carbon fixation via photosynthesis and nitrogen assimilation via ammonium uptake in rice.

Phosphorus (P) is an essential element for plant growth and development. Vacuoles play a fundamental role in the storage and remobilization of P in plants, while our understanding of the evolutionary mechanisms of creating and reusing P stores are limited. Besides, we also know very little about the coordination of intercellular P translocation, neither the inorganic phosphate (Pi) signaling nor the Pi transport patterns. Here we summarize recent advances in understanding the core elements involved in cellular and/or subcellular P homeostasis and signaling in unicellular green algae and multicellular land plants. We also propose further work that might help to uncover the high-resolution intracellular and intercellular landscape of Pi distribution and signaling in plants.

Background Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina’s high-throughput small RNA sequencing and transcriptome sequencing. Results The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. Conclusion These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.

Transient changes in intracellular Ca(2+) concentration have been well recognized to act as cell signals coupling various environmental stimuli to appropriate physiological responses with accuracy and specificity in plants. Calmodulin (CaM) and calmodulin-like proteins (CMLs) are major Ca(2+) sensors, playing critical roles in interpreting encrypted Ca(2+) signals. Ca(2+)-loaded CaM/CMLs interact and regulate a broad spectrum of target proteins such as channels/pumps/antiporters for various ions, transcription factors, protein kinases, protein phosphatases, metabolic enzymes, and proteins with unknown biochemical functions. Many of the target proteins of CaM/CMLs directly or indirectly regulate plant responses to environmental stresses. Basic information about stimulus-induced Ca(2+) signal and overview of Ca(2+) signal perception and transduction are briefly discussed in the beginning of this review. How CaM/CMLs are involved in regulating plant responses to abiotic stresses are emphasized in this review. Exciting progress has been made in the past several years, such as the elucidation of Ca(2+)/CaM-mediated regulation of AtSR1/CAMTA3 and plant responses to chilling and freezing stresses, Ca(2+)/CaM-mediated regulation of CAT3, MAPK8 and MKP1 in homeostasis control of reactive oxygen species signals, discovery of CaM7 as a DNA-binding transcription factor regulating plant response to light signals. However, many key questions in Ca(2+)/CaM-mediated signaling warrant further investigation. Ca(2+)/CaM-mediated regulation of most of the known target proteins is presumed based on their interaction. The downstream targets of CMLs are mostly unknown, and how specificity of Ca(2+) signaling could be realized through the actions of CaM/CMLs and their target proteins is largely unknown. Future breakthroughs in Ca(2+)/CaM-mediated signaling will not only improve our understanding of how plants respond to environmental stresses, but also provide the knowledge base to improve stress-tolerance of crops.

Calcium ion (Ca ) is a universal second messenger that plays a critical role in plant responses to diverse physiological and environmental stimuli. The stimulus-specific signals are perceived and decoded by a series of Ca binding proteins serving as Ca sensors. The majority of Ca sensors possess the EF-hand motif, a helix-loop-helix structure which forms a turn-loop structure. Although EF-hand proteins in model plant such as Arabidopsis have been well described, the identification, classification, and the physiological functions of EF-hand-containing proteins from soybean are not systemically reported. In this study, a total of at least 262 genes possibly encoding proteins containing one to six EF-hand motifs were identified in soybean genome. These genes include 6 calmodulins (CaMs), 144 calmodulin-like proteins (CMLs), 15 calcineurin B-like proteins, 50 calcium-dependent protein kinases (CDPKs), 13 CDPK-related protein kinases, 2 Ca - and CaM-dependent protein kinases, 17 respiratory burst oxidase homologs, and 15 unclassified EF-hand proteins. Most of these genes (87.8%) contain at least one kind of hormonal signaling- and/or stress response-related -elements in their -1500 bp promoter regions. Expression analyses by exploring the published microarray and Illumina transcriptome sequencing data revealed that the expression of these EF-hand genes were widely detected in different organs of soybean, and nearly half of the total EF-hand genes were responsive to various environmental or nutritional stresses. Quantitative RT-PCR was used to confirm their responsiveness to several stress treatments. To confirm the Ca -binding ability of these EF-hand proteins, four CMLs (CML1, CML13, CML39, and CML95) were randomly selected for SDS-PAGE mobility-shift assay in the presence and absence of Ca . Results showed that all of them have the ability to bind Ca . This study provided the first comprehensive analyses of genes encoding for EF-hand proteins in soybean. Information on the classification, phylogenetic relationships and expression profiles of soybean EF-hand genes in different tissues and under various environmental and nutritional stresses will be helpful for identifying candidates with potential roles in Ca signal-mediated physiological processes including growth and development, plant-microbe interactions and responses to biotic and abiotic stresses.

Biological nitrification inhibitors (BNIs) are released from plant roots as exudates to repress nitrifier activity in agricultural soils, and this can improve nitrogen (N) recovery from fertilizer and enhance the N-use-efficiency (NUE). This review summarizes the current understanding of the regulatory mechanisms of BNIs release from roots of plants, such as Brachiaria humidicola (pasture grasses), Sorghum bicolor (hybrid sorghum) and Oryza sativa (paddy rice). BNIs can be categorized as hydrophilic- and hydrophobic-BNIs. Root systems can rapidly release hydrophilic-BNIs when NH4+ is present in rhizosphere in combination with low pH, which is associated with the activation of plasma membrane H+-ATPase. Since plasma membrane H+-ATPase is responsible for the establishment of membrane potential and generation of proton motive force for the secondary transport of various substances. The BNIs release may probably occur through the voltage-gated anion channels by the membrane potential variation or via secondary transporters, most likely MATE transporters, powered by the proton motive force. In addition, ATP-binding cassette (ABC) transporters may be also involved in the active efflux of hydrophilic-BNIs. On the contrary, the release of the hydrophobic BNIs, such as sorgoleone, from plant roots may be mediated by the vesicle traffic process and/or exocytosis. In addition, the possible effects of various environmental factors on the BNIs release in soils have been discussed. Future research should focus on the identification of the corresponding BNIs transporters in plants, and this may be helpful for the application of BNI crops in the agricultural practice via breeding and genetic modification.

Plasma membrane (PM) H+-ATPase is a master enzyme involved in various plant physiological processes, such as stomatal movements in leaves and nutrient uptake and transport in roots. Overexpression of Oryza sativa PM H+-ATPase 1 (OSA1) has been known to increase NH4+ uptake in rice roots. Although electrophysiological and pharmacological experiments have shown that the transport of many substances is dependent on the proton motive force provided by PM H+-ATPase, the exact role of PM H+-ATPase on the uptake of nutrients in plant roots, especially for the primary macronutrients N, P, and K, is still largely unknown. Here, we used OSA1 overexpression lines (OSA1-oxs) and gene-knockout osa1 mutants to investigate the effect of modulation of PM H+-ATPase on the absorption of N, P, and K nutrients through the use of a nutrient-exhaustive method and noninvasive microtest technology (NMT) in rice roots. Our results showed that under different concentrations of P and K, the uptake rates of P and K were enhanced in OSA1-oxs; by contrast, the uptake rates of P and K were significantly reduced in roots of osa1 mutants when compared with wild-type. In addition, the net influx rates of NH4+ and K+, as well as the efflux rate of H+, were enhanced in OSA1-oxs and suppressed in osa1 mutants under low concentration conditions. In summary, this study indicated that overexpression of OSA1 stimulated the uptake rate of N, P, and K and promoted flux rates of cations (i.e., H+, NH4+, and K+) in rice roots. These results may provide a novel insight into improving the coordinated utilization of macronutrients in crop plants.

Background Plants must acquire at least 14 mineral nutrients from the soil to complete their life cycles. Insufficient availability or extreme high levels of the nutrients significantly affect plant growth and development. Plants have evolved a series of mechanisms to adapt to unsuitable growth conditions where nutrient levels are too low or too high. microRNAs (miRNAs), a class of small RNAs, are known to mediate post-transcriptional regulation by transcript cleavage or translational inhibition. Besides regulating plant growth and development, miRNAs are well documented to regulate plant adaptation to adverse environmental conditions including nutrient stresses. Scope In this review, we focus on recent progress in our understanding of how miRNAs are involved in plant response to stresses resulting from deficiency in nutrients, such as nitrogen, phosphorus, sulfur, copper and iron, as well as toxicities from heavy metal ions. Conclusions Accumulated evidence indicates that miRNAs play critical roles in sensing the abundance of nutrients, controlling nutrient uptake and phloem-mediated long-distance transport, and nutrient homeostasis. miRNAs act as systemic signals to coordinate these physiological activities helping plants respond to and survive nutrient stresses and toxicities. Knowledge about how miRNAs are involved in plant responses to nutrient stresses promise to provide novel strategies to develop crops with improved nutrient use efficiency which could be grown in soils with either excessive or insufficient availability of nutrients.

AIMS: Soybean is an important food crop as well as a promising energy source. Because soybean is self-sufficient in nitrogen, phosphorus, in the orthophosphate form (Pi), becomes the most limiting macronutrient affecting the growth and productivity of soybean, especially in acidic and alkaline soils. It has been documented that plants have developed a series of physiological and biochemical strategies to adapt to Pi deficiency, but the mechanistic details of soybean response to Pi deficiency, especially those at the molecular level, are largely unknown. In this study, we aim to understand how soybean plants respond to Pi deficiency in soils by identifying and analysing Pi-responsive genes in the roots of soybean at the whole-genome scale. METHODS: The transcriptome in soybean roots under Pi-deficiency was analyzed using the Illumina’s digital gene expression (DGE) high-throughput sequencing platforms, and the expression profiles of arbitrarily selected Pi-responsive genes identified in the current research were validated by quantitative RT-PCR. RESULTS: A total of 1612 genes were found to be differentially expressed in soybean roots after Pi deficiency for seven days; 727 genes were up-regulated, and 885 genes were down-regulated. Gene ontology (GO) enrichment analysis showed that 17 GO terms of biological processes were significantly enriched including photosynthesis, iron ion transport, dUTP metabolism, cell wall organization, fatty acid metabolism and stress responses. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, homeostasis control of reactive oxygen species, calcium signaling, hormonal signaling and gene transcription were included in the differentially expressed genes. Quantitative RT-PCR was used to analyze the expression of 30 arbitrarily selected genes and 29 of them were confirmed to exhibit similar differential expression patterns under Pi deficiency as revealed by the high throughput DGE sequencing. CONCLUSIONS: These results provide useful information for identifying and characterizing important components in the Pi signaling network in soybean and enhance understanding of the molecular mechanisms by which plants adapt to low Pi stress.

AIMS: Sorghum (Sorghum bicolor) roots release biological nitrification inhibitors (BNIs) to suppress soil nitrification. Presence of NH₄ ⁺ in the rhizosphere stimulates BNIs release and it is hypothesized to be functionally associated with plasma membrane (PM) H⁺-ATPase activity. However, whether the H⁺-ATPase is regulated at the transcriptional level, and if so, which isoforms of the H⁺-ATPases are involved in BNIs release are not known. Also, it is not clear whether the stimulation on BNIs release from roots is due to NH₄ ⁺ uptake or its assimilation, which are addressed in this study. METHODS: Root exudates from intact sorghum plants were collected using aerated solutions of NH₄ ⁺ or methyl-ammonium (MeA); and the BNI-activity release was determined. PM vesicles were isolated from fresh roots using a two-phase partitioning system; and the hydrolytic H⁺-ATPase activity was determined. All genes encoding PM H⁺-ATPases were searched in sorghum genome, and their expression in response to NH₄ ⁺ or MeA were analyzed by quantitative RT-PCR in sorghum roots. RESULTS: BNIs release and PM H⁺-ATPase activity increased with NH₄ ⁺ concentration (≤1.0 mM) in the root-exudate collection solutions, but at higher concentrations, it did not respond further or declined in case of the PM H⁺-ATPase activity. Twelve PM H⁺-ATPase genes were identified in sorghum genome; and these isoforms were designated SbA1 to SbA12. Five H⁺-ATPase genes were stimulated by NH₄ ⁺ in the rhizosphere, and have similar expression pattern, which is consistent with the variation in H⁺-ATPase activity. MeA, a non-metabolizable analogue of NH₄ ⁺, had no significant effects on BNIs release, H⁺-ATPase activity, or expression of the H⁺-ATPase genes. CONCLUSIONS: Our results suggest that the functional link between PM H⁺-ATPase activity and BNIs release is evident only at NH₄ ⁺ levels of ≤1.0 mM in the rhizosphere. The variation in PM H⁺-ATPase activity by NH₄ ⁺ is due to transcriptional regulation of five isoforms of the H⁺-ATPases. The stimulatory effect of NH₄ ⁺ on BNIs release is functionally associated with NH₄ ⁺ assimilation and not just with NH₄ ⁺ uptake alone.