The Transcription Factor MYB59 Regulates K+/NO3 - Translocation in the Arabidopsis Response to Low K+ Stress

The MdWRKY17 positively regulates nitrate uptake by promoting MdNRT2.5 expression under long-term low N stress in apple

Nitrogen (N) supply is critical for apple yield and quality. Improving nitrogen use efficiency (NUE) could reduce fertilizer application for maintaining apple yield at the cost of environmental pollution in infertile soil. The molecular mechanisms underlying nitrate (NO3-) uptake are foundational for breeding high NUE cultivars. The two-month low N treatment mimicking infertile soil dramatically induced the accumulation of transcription factor MdWRKY17 in apple. Overexpression of MdWRKY17 conferred enhanced long-term low nitrogen tolerance in transgenic apple plants and calli, while RNA interference of MdWRKY17 reduced this tolerance. MdNRT2.5 encoding a high-affinity nitrate transporter was identified by chromatin immunoprecipitation sequencing (ChIP-seq) as the direct target of MdWRKY17. This is confirmed by in vitro EMSA and in vivo ChIP-qPCR assay. Notably, overexpression of MdNRT2.5 increased NO3- uptake under long-term N-deficiency conditions. RNA interference of MdNRT2.5 in roots decreased NO3- uptake efficiency of MdWRKY17-OE transgenic apple plants, indicating that MdWRKY17 improves NO3- uptake mainly by activating MdNRT2.5 expression. Our study identified an important MdWRKY17-MdNRT2.5 module in response to long-term low N stress, which will contribute to the molecular breeding of high NUE apple cultivars.

The transcription factor OsNAC25 regulates potassium homeostasis in rice

Over-application of potassium (K) fertilizer in fields has a negative impact on the environment. Developing rice varieties with high KUE will reduce fertilizer for sustainable agriculture. However, the genetic basis of KUE in a more diverse and inclusive population remains largely unexplored. Here, we show that the transcription factor OsNAC25 enhances K+ uptake and confers high KUE under low K+ supply. Disruption of OsNAC25 by CRISPR/Cas9-mediated mutagenesis led to a considerable loss of K+ uptake capacity in rice roots, coupled with reduced K+ accumulation in rice and severe plant growth defects under low- K+ conditions. However, the overexpression of OsNAC25 enhanced K+ accumulation by regulating proper K+ uptake capacity in rice roots. Further analysis displayed that OsNAC25 can bind to the promoter of OsSLAH3 to repress its transcription in response to low- K+ stress. Nucleotide diversity analyses suggested that OsNAC25 may be selected during japonica populations' adaptation of low K+ tolerance. Natural variation of OsNAC25 might cause differential expression in different haplotype varieties, thus conferring low K+ tolerance in the Hap 1 and Hap 4 -carrying varieties, and the japonica allele OsNAC25 could enhance low K+ tolerance in indica variety, conferring great potential to improve indica low K+ tolerance and grain development. Taken together, we have identified a new NAC regulator involved in rice low K+ tolerance and grain development, and provide a potential target gene for improving low K+ tolerance and grain development in rice.

Alternating inverse modulation of xylem K+/NO3 - loading by HY5 and PIF facilitates diurnal regulation of root-to-shoot water and nutrient transport

Diurnal light-dark cycles regulate nutrient uptake and transport; however, the underlying molecular mechanisms remain largely unknown. Transcription factor MYB59 and ion transporter NPF7.3 participate in root-to-shoot K+/NO3 - translocation in Arabidopsis. In this study, transcriptional analyses and western blotting experiments revealed the diurnal expression of the MYB59-NPF7.3 module. ChIP-qPCR and EMSA showed that transcription factors HY5 and PIF directly bind to the MYB59 promoter. Phenotype analyses and ion content measurement indicated that HY5 and PIF antagonistically control root-to-shoot K+/NO3 - translocation through the MYB59-NPF7.3 module. We found HY5 proteins accumulate in roots and repress MYB59 transcription during daytime, while PIF proteins promote MYB59 transcription in the dark. The expression levels of the NPF7.3 transcript and protein are gradually decreased during daytime, but increased at night. The enhancement of K+/NO3 - loading into the xylem mediated by NPF7.3 could increase root pressure at night, which maintained the root-to-shoot water/nutrient translocation. This study reveals a synergistic mechanism between light signaling and nutrient transport in plants, and defines a diurnal molecular switch of driving forces for root-to-shoot water/nutrient translocation.

ZmNPF7.10 confers potassium and nitrogen distribution from node to leaf in maize

In graminaceous plants, nodes play vital roles in nutrient allocation, especially for preferential nutrient distribution to developing leaves and reproductive organs. However, the molecular mechanisms underlying this distribution remain poorly understood. In this study, we identified a transporter named ZmNPF7.10 that is involved in potassium (K) and nitrogen (N) distribution in maize nodes. In Xenopus oocytes, ZmNPF7.10 showed NO3 - and K+ transport activity in a pH-dependent manner. ZmNPF7.10 is predominantly expressed in the nodes at the reproductive growth stage, and preferentially expressed in the xylem parenchyma cells of enlarged vascular bundles (EVBs) in nodes. Disruption of ZmNPF7.10 resulted in the decline of K and N in leaves, but accumulation of K and N in nodes, suggesting ZmNPF7.10 conducts K and N distribution from nodes to leaves in maize. We identified a natural variant of 7.1-kb InDel in the promoter region that was significantly associated with ZmNPF7.10 transcript level in nodes, leaf K and N concentration, as well as grain yield. These findings demonstrate that ZmNPF7.10 functions as a dual role transporter that mediates K and N distribution in nodes. This study provides important insights into the molecular mechanisms of nutrient distribution in maize.

Transcription factor AtNAC002 positively regulates Cu toxicity tolerance in Arabidopsis thaliana

Copper (Cu) is an essential micronutrient for plant growth and development, but environmental Cu pollution has become increasingly severe, adversely affecting both ecosystems and crop productivity. In this study, we identified the AtNAC002 gene as a positive regulator of Cu toxicity in Arabidopsis thaliana. We found that AtNAC002 expression was induced by Cu excess, and the atnac002 mutant was Cu-sensitive, accumulating more Cu than the wild-type. Additionally, atnac002 mutants exhibit reduced activities of antioxidant enzymes (SOD, POD, and CAT), leading to increased levels of reactive oxygen species and malondialdehyde, which decrease Cu resistance. AtNAC002 might play a role in vacuolar and mitochondrial Cu compartmentalization by regulating genes involved in Cu detoxification, specifically COX11 and HCC1. Furthermore, AtNAC002 was implicated in flavone and flavanol biosynthesis, with the atnac002 mutant showing reduced flavonoid content. Our findings suggest that AtNAC002 is integral to the regulation of Cu toxicity tolerance in A. thaliana. This knowledge is critical for advancing our understanding and offers potential molecular breeding targets to enhance plant performance under Cu excess, which is significant for improving global food security and forest restoration.

Functional and biotechnological cues of potassium homeostasis for stress tolerance and plant development

Potassium (K+) is indispensable for the regulation of a plethora of functions like plant metabolism, growth, development, and abiotic stress responses. K+ is associated with protein synthesis and entangled in the activation of scores of enzymes, stomatal regulation, and photosynthesis. It has multiple transporters and channels that assist in the uptake, efflux, transport within the cell as well as from soil to different tissues, and the grain filling sites. While it is implicated in ion homeostasis during salt stress, it acts as a modulator of stomatal movements during water deficit conditions. K+ is reported to abate the effects of chilling and photooxidative stresses. K+ has been found to ameliorate effectively the co-occurrence of drought and high-temperature stresses. Nutrient deficiency of K+ makes leaves necrotic, leads to diminished photosynthesis, and decreased assimilate utilization highlighting the role it plays in photosynthesis. Notably, K+ is associated with the detoxification of reactive oxygen species (ROS) when plants are exposed to diverse abiotic stress conditions. It is irrefutable now that K+ reduces the activity of NADPH oxidases and at the same time maintains electron transport activity, which helps in mitigating the oxidative stress. K+ as a macronutrient in plant growth, the role of K+ during abiotic stress and the protein phosphatases involved in K+ transport have been reviewed. This review presents a holistic view of the biological functions of K+, its uptake, translocation, signaling, and the critical roles it plays under abiotic stress conditions, plant growth, and development that are being unraveled in recent times.

Transcription factor NtMYB59 targets NtMYB12 to negatively regulate the biosynthesis of polyphenols in Nicotiana tabacum

MYB12 is a key regulator that has been shown to promote the accumulation of various phenylpropanoid compounds in plants. However, the regulation of MYB12 gene is largely unknown. In this study, we found that overexpression of the NtMYB59 gene significantly inhibited the accumulation of chlorogenic acid (CGA), flavonols, and anthocyanins in tobacco, while knock-down and knock-out of NtMYB59 significantly increased the contents of these polyphenol compounds. Transcriptome analysis between WT and NtMYB59-OE plants revealed several differentially expressed genes (DEGs) encoding crucial enzymes in the phenylpropanoid pathway and the transcription factor NtMYB12. ChIP-seq assay further indicated that NtMYB12 might be a direct target of NtMYB59. Subsequent yeast one-hybrid, electrophoretic mobility shift assay, and Dual-Luciferase assays confirmed that NtMYB59 directly binds to the promoter of NtMYB12 to inhibit its expression. Moreover, loss-function of NtMYB59 significantly promoted the accumulation of flavonols and anthocyanins in ntmyb59, but their contents in ntmyb59/ntmyb12 double mutants were significantly lower than that of WT and ntmyb59 plants, indicating that the regulation of NtMYB59 on flavonoids biosynthesis depends on the activity of NtMYB12. Our study revealed that NtMYB59 regulates the expression of NtMYB12, and provided new potential strategies for modulating phenylpropanoids biosynthesis in tobacco.

Physiological, biochemical, and transcriptomic alterations in Castor (Ricinus communis L.) under polyethylene glycol-induced oxidative stress

BACKGROUND

Castor is an important industrial raw material. Drought-induced oxidative stress leads to slow growth and decreased yields in castor. However, the mechanisms of drought-induced oxidative stress in castor remain unclear. Therefore, in this study, physiological, biochemical, and RNA-seq analyses were conducted on the roots of castor plants under PEG-6000 stress for 3 d and 7 d followed by 4 d of hydration.

RESULTS

The photosynthetic rate of castor leaves was inhibited under PEG-6000 stress for 3 and 7 d. Biochemical analysis of castor roots stressed for 3 d and 7 d, and rehydrated for 4 d revealed that the activities of APX and CAT were highest after only 3 d of stress, whereas the activities of POD, GR, and SOD peaked after 7 d of stress. RNA-seq analysis revealed 2926, 1507, and 111 differentially expressed genes (DEGs) in the roots of castor plants under PEG-6000 stress for 3 d and 7 d and after 4 d of rehydration, respectively. GO analysis of the DEGs indicated significant enrichment in antioxidant activity. Furthermore, KEGG enrichment analysis of the DEGs revealed significantly enriched metabolic pathways, including glutathione metabolism, fatty acid metabolism, and plant hormone signal transduction. WGCNA identified the core genes PP2C39 and GA2ox4 in the navajowhite1 module, which was upregulated under PEG-6000 stress. On the basis of these results, we propose a model for the response to drought-induced oxidative stress in castor.

CONCLUSIONS

This study provides valuable antioxidant gene resources, deepening our understanding of antioxidant regulation and paving the way for further molecular breeding of castor plants.

Small GTPase PvARFR2 interacts with cytosolic ABA receptor kinase 3 to enhance alkali tolerance in switchgrass

Soil alkalization has become a serious problem that limits plant growth through osmotic stress, ionic imbalance, and oxidative stress. Understanding how plants resist alkali stress has practical implications for alkaline-land utilization. In this study, we identified a small GTPase, PvARFR2 (ADP ribosylation factors related 2), that positively regulates alkali tolerance in switchgrass (Panicum virgatum) and uncovered its potential mode of action. Overexpressing PvARFR2 in switchgrass and Arabidopsis (Arabidopsis thaliana) conferred transformant tolerance to alkali stress, demonstrated by alleviated leaf wilting, less oxidative injury, and a lower Na+/K+ ratio under alkali conditions. Conversely, switchgrass PvARFR2-RNAi and its homolog mutant atgb1 in Arabidopsis displayed alkali sensitives. Transcriptome sequencing analysis showed that cytosolic abscisic acid (ABA) receptor kinase PvCARK3 transcript levels were higher in PvARFR2 overexpression lines compared to the controls and were strongly induced by alkali treatment in shoots and roots. Phenotyping analysis revealed that PvCARK3-OE × atgb1 lines were sensitive to alkali similar to the Arabidopsis atgb1 mutant, indicating that PvARFR2/AtGB1 functions in the same pathway as PvCARK3 under alkaline stress conditions. Application of ABA on PvARFR2-OE and PvCARK3-OE switchgrass transformants resulted in ABA sensitivity. Moreover, we determined that PvARFR2 physically interacts with PvCARK3 in vitro and in vivo. Our results indicate that a small GTPase, PvARFR2, positively responds to alkali stress by interacting with the cytosolic ABA receptor kinase PvCARK3, connecting the alkaline stress response to ABA signaling.

Nitrate transporters and mechanisms of nitrate signal transduction in Arabidopsis and rice

Nitrate (NO3 -) is a significant inorganic nitrogen source in soil, playing a crucial role in influencing crop productivity. As sessile organisms, plants have evolved complex mechanisms for nitrate uptake and response to varying soil levels. Recent advancements have enhanced our understanding of nitrate uptake and signaling pathways. This mini-review offers a comparative analysis of nitrate uptake mechanisms in Arabidopsis and rice. It also examines nitrate signal transduction, highlighting the roles of AtNRT1.1 and AtNLP7 as nitrate receptors and elucidating the OsNRT1.1B-OsSPX4-OsNLP3 cascade. Additionally, it investigates nuclear transcriptional networks that regulate nitrate-responsive genes, controlled by various transcription factors (TFs) crucial for plant development. By integrating these findings, we highlight mechanisms that may help to enhance crop nitrogen utilization.

WRKY6 transcription factor modulates root potassium acquisition through promoting expression of AKT1 in Arabidopsis

Potassium (K+), being an essential macronutrient in plants, plays a central role in many aspects. Root growth is highly plastic and is affected by many different abiotic stresses including nutrient deficiency. The Shaker-type K+ channel Arabidopsis (Arabidopsis thaliana) K+ Transporter 1 (AKT1) is responsible for K+ uptake under both low and high external K+ conditions. However, the upstream transcription factor of AKT1 is not clear. Here, we demonstrated that the WRKY6 transcription factor modulates root growth to low potassium (LK) stress in Arabidopsis. WRKY6 showed a quick response to LK stress and also to many other abiotic stress treatments. The two wrky6 T-DNA insertion mutants were highly sensitive to LK treatment, whose primary root lengths were much shorter, less biomass and lower K+ content in roots than those of wild-type plants, while WRKY6-overexpression lines showed opposite phenotypes. A further investigation showed that WRKY6 regulated the expression of the AKT1 gene via directly binding to the W-box elements in its promoter through EMSA and ChIP-qPCR assays. A dual luciferase reporter analysis further demonstrated that WRKY6 enhanced the transcription of AKT1. Genetic analysis further revealed that the overexpression of AKT1 greatly rescued the short root phenotype of the wrky6 mutant under LK stress, suggesting AKT1 is epistatic to WRKY6 in the control of LK response. Further transcriptome profiling suggested that WRKY6 modulates LK response through a complex regulatory network. Thus, this study unveils a transcription factor that modulates root growth under potassium deficiency conditions by affecting the potassium channel gene AKT1 expression.

Integrated analyses of ionomics, phytohormone profiles, transcriptomics, and metabolomics reveal a pivotal role of carbon-nano sol in promoting the growth of tobacco plants

BACKGROUND

Carbon nano sol (CNS) can markedly affect the plant growth and development. However, few systematic analyses have been conducted on the underlying regulatory mechanisms in plants, including tobacco (Nicotiana tabacum L.).

RESULTS

Integrated analyses of phenome, ionome, transcriptome, and metabolome were performed in this study to elucidate the physiological and molecular mechanisms underlying the CNS-promoting growth of tobacco plants. We found that 0.3% CNS, facilitating the shoot and root growth of tobacco plants, significantly increased shoot potassium concentrations. Antioxidant, metabolite, and phytohormone profiles showed that 0.3% CNS obviously reduced reactive oxygen species production and increased antioxidant enzyme activity and auxin accumulation. Comparative transcriptomics revealed that the GO and KEGG terms involving responses to oxidative stress, DNA binding, and photosynthesis were highly enriched in response to exogenous CNS application. Differential expression profiling showed that NtNPF7.3/NtNRT1.5, potentially involved in potassium/auxin transport, was significantly upregulated under the 0.3% CNS treatment. High-resolution metabolic fingerprints showed that 141 and 163 metabolites, some of which were proposed as growth regulators, were differentially accumulated in the roots and shoots under the 0.3% CNS treatment, respectively.

CONCLUSIONS

Taken together, this study revealed the physiological and molecular mechanism underlying CNS-mediated growth promotion in tobacco plants, and these findings provide potential support for improving plant growth through the use of CNS.

Arbuscular Mycorrhizal Fungi Improve Lycium barbarum Potassium Uptake by Activating the Expression of LbHAK

Arbuscular mycorrhizal (AM) fungi can establish a mutualistic relationship with the roots of most terrestrial plants to increase plant nutrient uptake. The effects of potassium uptake and transport by AM symbiosis are much less reported compared to other nutrients. In this research, a heterologous yeast system was used to verify that the LbHAK has capacity for potassium uptake. The split-roots system implemented using seedlings of Lycium barbarum confirmed that R. irregularis locally induced LbHAK expression, which means that LbHAK is only expressed in mycorrhizal roots. Furthermore, the impacts of overexpression of LbHAK on the growth, nutrients and water uptake, and transport of mycorrhizal tobacco (inoculation with Rhizophagus irregularis) at 0.2 mM and 2 mM K conditions were assessed. The mycorrhizal tobacco growth and potassium accumulation were significantly enhanced through LbHAK overexpression in tobacco. In addition, overexpression of LbHAK substantially enhanced phosphorus content, while stimulating the expression of NtPT4, Rir-AQP1, and Rir-AQP2 in mycorrhizal tobacco. Moreover, LbHAK overexpression greatly promoted AM colonization. LbHAK has a potential role in facilitating potassium absorption through the mycorrhizal pathway, and overexpression of LbHAK in tobacco may promote the transport of potassium, phosphorus, and water from AM fungi to tobacco. These data imply the important roles played by the LbHAK in AM-fungi-induced potassium uptake in L. barbarum and in improving plant nutrients and AM colonization.

An alfalfa MYB-like transcriptional factor MsMYBH positively regulates alfalfa seedling drought resistance and undergoes MsWAV3-mediated degradation

Drought is a major threat to alfalfa (Medicago sativa L.) production. The discovery of important alfalfa genes regulating drought response will facilitate breeding for drought-resistant alfalfa cultivars. Here, we report a genome-wide association study of drought resistance in alfalfa. We identified and functionally characterized an MYB-like transcription factor gene (MsMYBH), which increases the drought resistance in alfalfa. Compared with the wild-types, the biomass and forage quality were enhanced in MsMYBH overexpressed plants. Combined RNA-seq, proteomics and chromatin immunoprecipitation analysis showed that MsMYBH can directly bind to the promoters of MsMCP1, MsMCP2, MsPRX1A and MsCARCAB to improve their expression. The outcomes of such interactions include better water balance, high photosynthetic efficiency and scavenge excess H2O2 in response to drought. Furthermore, an E3 ubiquitin ligase (MsWAV3) was found to induce MsMYBH degradation under long-term drought, via the 26S proteasome pathway. Furthermore, variable-number tandem repeats in MsMYBH promoter were characterized among a collection of germplasms, and the variation is associated with promoter activity. Collectively, our findings shed light on the functions of MsMYBH and provide a pivotal gene that could be leveraged for breeding drought-resistant alfalfa. This discovery also offers new insights into the mechanisms of drought resistance in alfalfa.

Differential Morpho-Physiological, Ionomic, and Phytohormone Profiles, and Genome-Wide Expression Profiling Involving the Tolerance of Allohexaploid Wheat (Triticum aestivum L.) to Nitrogen Limitation

Common wheat (Triticum aestivum L.) is a global staple food, while nitrogen (N) limitation severely hinders plant growth, seed yield, and grain quality of wheat. Genetic variations in the responses to low N stresses among allohexaploid wheat (AABBDD, 2n = 6x = 42) genotypes emphasize the complicated regulatory mechanisms underlying low N tolerance and N use efficiency (NUE). In this study, hydroponic culture, inductively coupled plasma mass spectrometry, noninvasive microtest, high-performance liquid chromatography, RNA-seq, and bioinformatics were used to determine the differential growth performance, ionome and phytohormone profiles, and genome-wide expression profiling of wheat plants grown under high N and low N conditions. Transcriptional profiling of NPFs, NRT2s, CLCs, SLACs/SLAHs, AAPs, UPSs, NIAs, and GSs characterized the core members, such as TaNPF6.3-6D, TaNRT2.3-3D, TaNIA1-6B, TaGLN1;2-4B, TaAAP14-5A/5D, and TaUPS2-5A, involved in the efficient transport and assimilation of nitrate and organic N nutrients. The low-N-sensitivity wheat cultivar XM26 showed obvious leaf chlorosis and accumulated higher levels of ABA, JA, and SA than the low-N-tolerant ZM578 under N limitation. The TaMYB59-3D-TaNPF7.3/NRT1.5-6D module-mediated shoot-to-root translocation and leaf remobilization of nitrate was proposed as an important pathway regulating the differential responses between ZM578 and XM26 to low N. This study provides some elite candidate genes for the selection and breeding of wheat germplasms with low N tolerance and high NUE.

The Molecular Mechanism of Potassium Absorption, Transport, and Utilization in Rice

Potassium is essential for plant growth and development and stress adaptation. The maintenance of potassium homeostasis involves a series of potassium channels and transporters, which promote the movement of potassium ions (K+) across cell membranes and exhibit complex expression patterns and regulatory mechanisms. Rice is a major food crop in China. The low utilization rate of potassium fertilizer limits the yield and quality of rice. Elucidating the molecular mechanisms of potassium absorption, transport, and utilization is critical in improving potassium utilization efficiency in rice. Although some K+ transporter genes have been identified from rice, research on the regulatory network is still in its infancy. Therefore, this review summarizes the relevant information on K+ channels and transporters in rice, covering the absorption of K+ in the roots, transport to the shoots, the regulation pathways, the relationship between K+ and the salt tolerance of rice, and the synergistic regulation of potassium, nitrogen, and phosphorus signals. The related research on rice potassium nutrition has been comprehensively reviewed, the existing research foundation and the bottleneck problems to be solved in this field have been clarified, and the follow-up key research directions have been pointed out to provide a theoretical framework for the cultivation of potassium-efficient rice.

Overexpression of a nitrate transporter NtNPF2.11 increases nitrogen accumulation and yield in tobacco

Nitrogen (N) is the key essential macronutrient for crop growth and yield. Over-application of inorganic N fertilizer in fields generated serious environmental pollution and had a negative impact to human health. Therefore, improving crop N use efficiency (NUE) is helpful for sustainable agriculture. The biological functions of nitrogen transporters and regulators have been intensively studied in many crop species. However, only a few nitrogen transporters have been identified in tobacco to date. We reported the identification and functional characterization of a nitrate transporter NtNPF2.11 from tobacco (Nicotiana tabacum). qRT-PCR assay revealed that NtNPF2.11 was mainly expressed in leaf and vein. Under middle N (MN, 1.57 kg N/100 m2) and high N (HN, 2.02 kg N/100 m2) conditions, overexpression of NtNPF2.11 in tobacco greatly improved N utilization and biomass. Moreover, under middle N and high N conditions, the expression of genes for nitrate assimilation, such as NtNR1, NtNiR, NtGS and NtGOGAT, were upregulated in NtNPF2.11 overexpression plants. Compared with WT, overexpression of NtNPF2.11 increased potassium (K) accumulation under high N conditions. These results indicated that overexpression of NtNPF2.11 could increase tobacco yield, N and K accumulation under higher N conditions. Overall, these findings improve our understanding the function of NtNPF2.11 and provide useful gene for sustainable agriculture.

The K+ transporter NPF7.3/NRT1.5 and the proton pump AHA2 contribute to K+ transport in Arabidopsis thaliana under K+ and NO3- deficiency

Nitrate (NO3 -) and potassium (K+) are distributed in plants via short and long-distance transport. These two pathways jointly regulate NO3 - and K+ levels in all higher plants. The Arabidopsis thaliana transporter NPF7.3/NRT1.5 is responsible for loading NO3 - and K+ from root pericycle cells into the xylem vessels, facilitating the long-distance transport of NO3 - and K+ to shoots. In this study, we demonstrate a protein-protein interaction of NPF7.3/NRT1.5 with the proton pump AHA2 in the plasma membrane by split ubiquitin and bimolecular complementation assays, and we show that a conserved glycine residue in a transmembrane domain of NPF7.3/NRT1.5 is crucial for the interaction. We demonstrate that AHA2 together with NRT1.5 affects the K+ level in shoots, modulates the root architecture, and alters extracellular pH and the plasma membrane potential. We hypothesize that NRT1.5 and AHA2 interaction plays a role in maintaining the pH gradient and membrane potential across the root pericycle cell plasma membrane during K+ and/or NO3 - transport.

Role of Potassium-Dependent Alternative Splicing of MYB59 in the Maintenance of Potassium Concentration in Shoots of Arabidopsis thaliana

Potassium (K) is a major plant nutrient. K+ is taken up by channel and transporter proteins in roots and translocated from roots to shoots via the xylem. In Arabidopsis thaliana, the K+ transporter NPF7.3 mediates K+ loading into the xylem and the transcription factor MYB59 is responsible for NPF7.3 expression. Here, we demonstrate that MYB59 is regulated by alternative splicing in response to K availability. Three splicing isoforms of MYB59 are detected in roots: an isoform with the first intron spliced out encodes a protein with the full DNA-binding motif (MYB59α), and two isoforms with the first intron retained partially or completely encode a protein missing part of the DNA-binding motif (MYB59β). Functional analysis showed that only MYB59α is capable of inducing the expression of NPF7.3. The abundance of the MYB59α isoform increased under low K, but the total abundance of MYB59 transcripts did not change, indicating that MYB59α is increased by modification of the splicing pattern in response to low K. Although MYB59α is increased by low K, NPF7.3 expression remained constant independent of K. In addition, there was no significant difference in NPF7.3 expression between an MYB59 knockout mutant and the wild type under normal K. These results suggest that an unknown mechanism is involved in NPF7.3 expression under normal K and switches roles with MYB59 under low K. We propose that the regulation of MYB59 by alternative splicing is required for the maintenance of shoot K concentration in adaptation to low K.

Anatomical and Transcriptome Analyses of Moso Bamboo Culm Neck Growth: Unveiling Key Insights

The Moso bamboo culm neck, connected with the rhizome and the shoot bud, is an important hub for connecting and transporting the aboveground and belowground systems of bamboo for the shoot bud development and rapid growth. Our previous study revealed that the culm neck generally undergoes six different developmental stages (CNS1-CNS6), according to the primary thickening growth of the underground shoot bud. However, the molecular mechanism of the culm neck development remains unknown. The present study focused on the developmental process of the CNS3-CNS5 stages, representing the early, middle, and late elongation stages, respectively. These stages are densely packed with vascular tissues and consist of epidermis, hypodermis, cortex, and ground tissue. Unlike the hollow structure of the culms, the culm necks are solid structures. As the culm neck continues to grow, the lignin deposition increases noticeably, contributing to its progressive strengthening. For the transcriptome analysis, a total of 161,160 transcripts with an average length of 2373 were obtained from these stages using both PacBio and Illumina sequencing. A total of 92.2% of the reads mapped to the Moso bamboo reference genome. Further analysis identified a total of 5524 novel genes and revealed a dynamic transcriptome. Secondary-metabolism- and transport-related genes were upregulated particularly with the growth of the culm neck. Further analysis revealed the molecular processes of lignin accumulation in the culm neck, which include differentially expressed genes (DEGs) related to cell wall loosening and remodeling and secondary metabolism. Moreover, the upregulations of transcription factors such as MYBH and RSM in the MYB family play crucial roles during critical transitions in the culm neck development, such as changes in the angle between the rhizome and the culm neck. Our new findings provide essential insights into the cellular roadmaps, transcriptional networks, and key genes involved in the culm neck development.

Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction

Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.

The Chemical Composition and Transcriptome Analysis Reveal the Mechanism of Color Formation in Tea (Camellia sinensis) Pericarp

To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. Jinxuan), and Baitangziya (Camellia sinensis L. var. Baitang). Results of biochemical analysis revealed that low chlorophyll content and low chlorophyll/carotene ratio may be the biochemical basis for albino characteristics in the 'Zhongbaiyihao' pericarp. The differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, including DFR, F3'5'H, CCoAOMT, and 4-coumaroyl-CoA, were highly expressed in the purple 'Baitangziya' pericarp. In the chlorophyll synthesis of white pericarp, GUN5 (Genome Uncoupled 5) and 8-vinyl-reductase both showed high expression levels compared to the green one, which indicated that albino 'Zhongbaiyihao' pericarp had a higher chlorophyll synthesis capacity than 'Jinxuan'. Meanwhile, chlorophyllase (CLH, CSS0004684) was lower in 'Baitang' than in 'Jinxuan' and 'Zhongbaiyihao' pericarp. Among the differentially expressed transcription factors, MYB59, WRKY41-like2 (CS ng17509), bHLH62 like1 (CS ng6804), and bHLH62-like3 (CSS0039948) were downregulated in Jinxuan pericarp, suggesting that transcription factors played a role in regulating tea pericarp coloration. These findings provide a better understanding of the molecular mechanisms and theoretical basis for utilizing functional components of tea pericarp.

Integrating Transcriptional, Metabolic, and Physiological Responses to Drought Stress in Ilex paraguariensis Roots

The appearance of water stress episodes triggers leaf abscission and decreases Ilex paraguariensis yield. To explore the mechanisms that allow it to overcome dehydration, we investigated how the root gene expression varied between water-stressed and non-stressed plants and how the modulation of gene expression was linked to metabolite composition and physiological status. After water deprivation, 5160 differentially expressed transcripts were obtained through RNA-seq. The functional enrichment of induced transcripts revealed significant transcriptional remodelling of stress-related perception, signalling, transcription, and metabolism. Simultaneously, the induction of the enzyme 9-cis-expoxycarotenoid dioxygenase (NCED) transcripts reflected the central role of the hormone abscisic acid in this response. Consequently, the total content of amino acids and soluble sugars increased, and that of starch decreased. Likewise, osmotic adjustment and radical growth were significantly promoted to preserve cell membranes and water uptake. This study provides a valuable resource for future research to understand the molecular adaptation of I. paraguariensis plants under drought conditions and facilitates the exploration of drought-tolerant candidate genes.

Long-Term Impact of N, P, K Fertilizers in Different Rates on Yield and Quality of Anisodus tanguticus (Maxinowicz) Pascher

Anisodus tanguticus (Maxinowicz) Pascher (Solanaceae) is a traditional Chinese herb that is widely used in folklore and clinical practice. In recent years, wild populations have been severely impacted to the point of extinction due to over-harvesting and reclamation. Therefore, artificial cultivation is important to relieve the pressure of market demand and protect wild plant resources. Using a "3414" fertilization design, i.e., 3 factors (N, P, and K), 4 levels, and 14 fertilization treatments, with 3 replicates and a total of 42 experimental plots, A. tanguticus was harvested in October 2020, June 2021, August 2021, and October 2021, and the yield and alkaloid content were determined. The study aimed to provide a theoretical basis and technical reference for the standardization of A. tanguticus cultivation. Biomass accumulation and alkaloid content showed a trend of increasing and then decreasing with the application of nitrogen, phosphorus, and potassium, and the biomass accumulation was the highest at the application levels of nitrogen and phosphorus in T6 and T9 and at the application levels of medium and low potassium. The alkaloid content showed an increasing trend between October of the first year and June of the second year and a decreasing trend in the second year with the increase in the harvesting period. Yield and alkaloid yield showed a decreasing trend between October of the first year and June of the second year and an increasing trend in the second year with the increase in the harvesting period. The recommended application rates are 225-300 kg/ha² for nitrogen, 850-960 kg/ha² for phosphorus, and 65-85 kg/ha² for potassium.

An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus

Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the A_n- and C_n-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus.

The MYB59 transcription factor negatively regulates salicylic acid- and jasmonic acid-mediated leaf senescence

Leaf senescence is the final stage of leaf development and is affected by various exogenous and endogenous factors. Transcriptional regulation is essential for leaf senescence, however, the underlying molecular mechanisms remain largely unclear. In this study, we report that the transcription factor MYB59, which was predominantly expressed in early senescent rosette leaves, negatively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). RNA sequencing revealed a large number of differentially expressed genes involved in several senescence-related biological processes in myb59-1 rosette leaves. Chromatin immunoprecipitation and transient dual-luciferase reporter assays demonstrated that MYB59 directly repressed the expression of SENESCENCE ASSOCIATED GENE 18 and indirectly inhibited the expression of several other senescence-associated genes to delay leaf senescence. Moreover, MYB59 was induced by salicylic acid (SA) and jasmonic acid (JA). MYB59 inhibited SA production by directly repressing the expression of ISOCHORISMATE SYNTHASE 1 and PHENYLALANINE AMMONIA-LYASE 2 and restrained JA biosynthesis by directly suppressing the expression of LIPOXYGENASE 2, thus forming two negative feedback regulatory loops with SA and JA and ultimately delaying leaf senescence. These results help us understand the novel function of MYB59 and provide insights into the regulatory network controlling leaf senescence in Arabidopsis.

Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize

Excessive accumulation of chloride (Cl^-) in the aboveground tissues under saline conditions is harmful to crops. Increasing the exclusion of Cl^- from shoots promotes salt tolerance in various crops. However, the underlying molecular mechanisms remain largely unknown. In this study, we demonstrated that a type A response regulator (ZmRR1) modulates Cl^- exclusion from shoots and underlies natural variation of salt tolerance in maize. ZmRR1 negatively regulates cytokinin signaling and salt tolerance, likely by interacting with and inhibiting His phosphotransfer (HP) proteins that are key mediators of cytokinin signaling. A naturally occurring non-synonymous SNP variant enhances the interaction between ZmRR1 and ZmHP2, conferring maize plants with a salt-hypersensitive phenotype. We found that ZmRR1 undergoes degradation under saline conditions, leading to the release of ZmHP2 from ZmRR1 inhibition, and subsequently ZmHP2-mediated signaling improves salt tolerance primarily by promoting Cl^- exclusion from shoots. Furthermore, we showed that ZmMATE29 is transcriptionally upregulated by ZmHP2-mediated signaling under highly saline conditions and encodes a tonoplast-located Cl^- transporter that promotes Cl^- exclusion from shoots by compartmentalizing Cl^- into the vacuoles of root cortex cells. Collectively, our study provides an important mechanistic understanding of the cytokinin signaling-mediated promotion of Cl^- exclusion from shoots and salt tolerance and suggests that genetic modification to promote Cl^- exclusion from shoots is a promising route for developing salt-tolerant maize.

Major-effect quantitative trait locus qLKR4.1 encodes a phospholipase Dδ protein associated with low-K+ stress tolerance by promoting root length

qLKR4.1, controlling low K⁺ resistance in tomato, was fine-mapped to an interval of 67.5 kb on chromosome A04, and one gene encoding phospholipase Dδ was identified as a candidate gene. In plants, changes in root length are an important morphological response to low K⁺ (LK) stress; however, the underlying genetics in tomato remain unclear. Here, we combined bulked segregant analysis-based whole-genome sequencing, single-nucleotide polymorphism haplotyping, and fine genetic mapping to identify a candidate gene as a major-effect quantitative trait loci (QTL), i.e., qLKR4.1, which was associated with LK tolerance due to increased root elongation in the tomato line JZ34. Through multiple analyses, we found that Solyc04g082000 is the most likely candidate for qLKR4.1, which encodes phospholipase Dδ (PLDδ). Increased root elongation under LK in JZ34 may be attributed to a non-synonymous single-nucleotide polymorphism in the Ca²⁺-binding domain region of this gene. Solyc04g082000 increases root length through its PLDδ activity. Silencing of Solyc04g082000^Arg in JZ34 led to a significant decrease in root length compared with silencing of Solyc04g082000^His allele in JZ18 under LK conditions. Mutation of a Solyc04g082000 homologue in Arabidopsis, pldδ, resulted in decreased primary root lengths under LK conditions, compared to the wild type. Transgenic tomato expressing the qLKR4.1^Arg allele from JZ34 exhibited a significant increase in root length compared with the wild type expressing the allele from JZ18 under LK conditions. Taken together, our results confirm that the PLDδ gene Solyc04g082000 exerts important functions in increasing tomato root length and LK tolerance.

Overexpression of MYB-like transcription factor SiMYB30 from foxtail millet (Setaria italica L.) confers tolerance to low nitrogen stress in transgenic rice

Nitrogen fertilizers significantly increase crop yield; however, the negative impact of excessive nitrogen use on the environment and soil requires urgent attention. Improving crop nitrogen use efficiency (NUE) is crucial to increase yields and protect the environment. Foxtail millet (Setaria italica L.), a gramineous crop with significant tolerance to barren croplands, is an ideal model crop for studying abiotic stress resistance in gramineous crops. However, knowledge of the regulatory network for NUE in foxtail millet is fragmentary. Herein, we identified an R2R3-like MYB transcription factor in foxtail millet, SiMYB30, which belongs to MYB subfamily 17. The expression of SiMYB30 is responsive to low nitrogen (LN) concentration. Compared with wildtype Kitaake, seedlings of rice lines overexpressing SiMYB30 showed significantly increased shoot fresh and dry weights, plant height, and root area under LN treatment indoors. Consistently, overexpression of SiMYB30 in field experiments significantly increased grain and stem nitrogen contents, grain yield per plant, and stem weight in rice. Furthermore, qRT-PCR revealed that SiMYB30 effectively activated the expression of nitrogen uptake-related genes-OsNRT1, OsNRT1.1B, and OsNPF2.4-and nitrogen assimilation-related genes-OsGOGAT1, OsGOGAT2, and OsNIA2. Notably, SiMYB30 directly bound to the promoter of OsGOGAT2 and regulated its expression. These results highlight the novel and pivotal role of SiMYB30 in improving crop NUE.

Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency

Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.

R2R3 MYB transcription factor SbMYBHv33 negatively regulates sorghum biomass accumulation and salt tolerance

SbMYBHv33 negatively regulated biomass accumulation and salt tolerance in sorghum and Arabidopsis by regulating reactive oxygen species accumulation and ion levels. Salt stress is one of the main types of environmental stress leading to a reduction in crop yield worldwide. Plants have also evolved a variety of corresponding regulatory pathways to resist environmental stress damage. This study aimed to identify a SbMYBHv33 transcription factor that downregulates in salt, drought, and abscisic acid (ABA) in the salt-tolerant inbred line sorghum M-81E. The findings revealed that overexpression of SbMYBHv33 in sorghum significantly reduced sorghum biomass accumulation at the seedling stage and also salinity tolerance. Meanwhile, a heterologous transformation of Arabidopsis with SbMYBHv33 produced a similar phenotype. The loss of function of the Arabidopsis homolog of SbMYBHv33 resulted in longer roots and increased salt tolerance. Under normal conditions, SbMYBHV33 overexpression promoted the expression of ABA pathway genes in sorghum and inhibited growth. Under salt stress conditions, the gene expression of SbMYBHV33 decreased in the overexpressed lines, and the promotion of these genes in the ABA pathway was attenuated. This might be an important reason for the difference in growth and stress resistance between SbMYBHv33-overexpressed sorghum and ectopic expression Arabidopsis. Hence, SbMYBHv33 is an important component of sorghum growth and development and the regulation of salt stress response, and it could negatively regulate salt tolerance and biomass accumulation in sorghum.

Wheat potassium transporter TaHAK13 mediates K+ absorption and maintains potassium homeostasis under low potassium stress

Potassium (K) is an essential nutrient for plant physiological processes. Members of the HAK/KUP/KT gene family act as potassium transporters, and the family plays an important role in potassium uptake and utilization in plants. In this study, the TaHAK13 gene was cloned from wheat and its function characterized. Real-time quantitative PCR (RT-qPCR) revealed that TaHAK13 expression was induced by environmental stress and up-regulated under drought (PEG6000), low potassium (LK), and salt (NaCl) stress. GUS staining indicated that TaHAK13 was mainly expressed in the leaf veins, stems, and root tips in Arabidopsis thaliana, and expression varied with developmental stage. TaHAK13 mediated K⁺ absorption when heterologously expressed in yeast CY162 strains, and its activity was slightly stronger than that of a TaHAK1 positive control. Subcellular localization analysis illustrated that TaHAK13 was located to the plasma membrane. When c(K⁺) ≤0.01 mM, the root length and fresh weight of TaHAK13 transgenic lines (athak5/TaHAK13, Col/TaHAK13) were significantly higher than those of non-transgenic lines (athak5, Col). Non-invasive micro-test technology (NMT) indicated that the net K influx of the transgenic lines was also higher than that of the non-transgenic lines. This suggests that TaHAK13 promotes K⁺ absorption, especially in low potassium media. Membrane-based yeast two-hybrid (MbY2H) and luciferase complementation assays (LCA) showed that TaHAK13 interacted with TaNPF5.10 and TaNPF6.3. Our findings have helped to clarify the biological functions of TaHAK13 and established a theoretical framework to dissect its function in wheat.

Functional characterization of BdCIPK31 in plant response to potassium deficiency stress

Potassium (K) is one of the most essential macronutrients for plants. However, K+ is deficient in some cultivated soils. Hence, improving the efficiencies of K+ uptake and utilization is important for agricultural production. Ca2+ signaling pathways play an important role in regulation of K+ acquisition. In the present study, BdCIPK31, a Calcineurin B-like protein interacting protein kinase (CIPK) from Brachypodium distachyon, was found to be a potential positive regulator in plant response to low K+ stress. The expression of BdCIPK31 was responsive to K+-deficiency, and overexpression of BdCIPK31 conferred enhanced tolerance to low K+ stress in transgenic tobaccos. Furthermore, BdCIPK31 was demonstrated to promote the K+ uptake in root, and could maintain normal root growth under K+-deficiency conditions. Additionally, BdCIPK31 functioned in scavenging excess reactive oxygen species (ROS), reduced oxidative damage caused by low K+ stress. Collectively, our study indicates that BdCIPK31 is a vital regulatory component in K+-acquisition system in plants.

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses

Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.

MYB Transcription Factors Becoming Mainstream in Plant Roots

The function of the root system is crucial for plant survival, such as anchoring plants, absorbing nutrients and water from the soil, and adapting to stress. MYB transcription factors constitute one of the largest transcription factor families in plant genomes with structural and functional diversifications. Members of this superfamily in plant development and cell differentiation, specialized metabolism, and biotic and abiotic stress processes are widely recognized, but their roles in plant roots are still not well characterized. Recent advances in functional studies remind us that MYB genes may have potentially key roles in roots. In this review, the current knowledge about the functions of MYB genes in roots was summarized, including promoting cell differentiation, regulating cell division through cell cycle, response to biotic and abiotic stresses (e.g., drought, salt stress, nutrient stress, light, gravity, and fungi), and mediate phytohormone signals. MYB genes from the same subfamily tend to regulate similar biological processes in roots in redundant but precise ways. Given their increasing known functions and wide expression profiles in roots, MYB genes are proposed as key components of the gene regulatory networks associated with distinct biological processes in roots. Further functional studies of MYB genes will provide an important basis for root regulatory mechanisms, enabling a more inclusive green revolution and sustainable agriculture to face the constant changes in climate and environmental conditions.

Receptor-like protein kinase BAK1 promotes K+ uptake by regulating H+-ATPase AHA2 under low potassium stress

Potassium (K+) is one of the essential macronutrients for plant growth and development. However, the available K+ concentration in soil is relatively low. Plant roots can perceive low K+ (LK) stress, then enhance high-affinity K+ uptake by activating H+-ATPases in root cells, but the mechanisms are still unclear. Here, we identified the receptor-like protein kinase Brassinosteroid Insensitive 1-Associated Receptor Kinase 1 (BAK1) that is involved in LK response by regulating the Arabidopsis (Arabidopsis thaliana) plasma membrane H+-ATPase isoform 2 (AHA2). The bak1 mutant showed leaf chlorosis phenotype and reduced K+ content under LK conditions, which was due to the decline of K+ uptake capacity. BAK1 could directly interact with the AHA2 C terminus and phosphorylate T858 and T881, by which the H+ pump activity of AHA2 was enhanced. The bak1 aha2 double mutant also displayed a leaf chlorosis phenotype that was similar to their single mutants. The constitutively activated form AHA2Δ98 and phosphorylation-mimic form AHA2T858D or AHA2T881D could complement the LK sensitive phenotypes of both aha2 and bak1 mutants. Together, our data demonstrate that BAK1 phosphorylates AHA2 and enhances its activity, which subsequently promotes K+ uptake under LK conditions.

Systematic Investigation and Expression Profiles of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in Tea Plant (Camellia sinensis)

NRT1/PTR FAMILY (NPF) genes are characterized as nitrate and peptide transporters that played important roles in various substrates transport in plants. However, little is known about the NPF gene in tea plants. Here, a total of 109 CsNPF members were identified from the tea plant genome, and divided into 8 groups according to their sequence characteristics and phylogenetic relationship. Gene structure and conserved motif analysis supported the evolutionary conservation of CsNPFs. Many hormone and stress response cis-acting elements and transcription factor binding sites were found in CsNPF promoters. Syntenic analysis suggested that multiple duplication types contributed to the expansion of NPF gene family in tea plants. Selection pressure analysis showed that CsNPF genes experienced strong purifying selective during the evolution process. The distribution of NPF family genes revealed that 8 NPF subfamilies were formed before the divergence of eudicots and monocots. Transcriptome analysis showed that CsNPFs were expressed differently in different tissues of the tea plant. The expression of 20 CsNPF genes at different nitrate concentrations was analyzed, and most of those genes responded to nitrate resupply. Subcellular localization showed that both CsNPF2.3 and CsNPF6.1 were localized in the plasma membrane, which was consistent with the characteristics of transmembrane proteins involved in NO₃^- transport. This study provides a theoretical basis for further investigating the evolution and function of NPF genes.

MdMYB10 affects nitrogen uptake and reallocation by regulating the nitrate transporter MdNRT2.4-1 in the red flesh apple

Nitrate is the major nitrogen sources for higher plants. In addition to serving not only as a nutrient, it is also a signaling molecule that regulates plant growth and development. Although membrane-bound nitrate transporter/peptide transporters (NRT/PTR) have been extensively studied and shown to regulate nitrate uptake and movement, little is known about how these factors are regulated by the external nitrogen environment. Red flesh apple, the coloration of which is determined by the transcription factor MdMYB10, had higher nitrate uptake efficiency than non-red flesh apple. Nitrate assimilation and utilization were increased in red flesh apple cultivar, and comparative transcriptome analysis showed that the expression of genes encoding the NRT2s was increased in red flesh apple. In vitro and in vivo experiments showed that MdMYB10 directly bound to the MdNRT2.4-1 promoter to transcriptionally activate its expression, resulting in enhanced nitrate uptake. MdMYB10 also controlled nitrate reallocation from old leaves to new leaves through MdNRT2.4-1. Overall, our findings provide novel insights into the mechanism by which MdMYB10 controls nitrate uptake and reallocation in apple, which facilitates adaptation to low nitrogen environment.

COE2 Is Required for the Root Foraging Response to Nitrogen Limitation

There are numerous exchanges of signals and materials between leaves and roots, including nitrogen, which is one of the essential nutrients for plant growth and development. In this study we identified and characterized the Chlorophyll A/B-Binding Protein (CAB) (named coe2 for CAB overexpression 2) mutant, which is defective in the development of chloroplasts and roots under normal growth conditions. The phenotype of coe2 is caused by a mutation in the Nitric Oxide Associated (NOA1) gene that is implicated in a wide range of chloroplast functions including the regulation of metabolism and signaling of nitric oxide (NO). A transcriptome analysis reveals that expression of genes involved in metabolism and lateral root development are strongly altered in coe2 seedlings compared with WT. COE2 is expressed in hypocotyls, roots, root hairs, and root caps. Both the accumulation of NO and the growth of lateral roots are enhanced in WT but not in coe2 under nitrogen limitation. These new findings suggest that COE2-dependent signaling not only coordinates gene expression but also promotes chloroplast development and function by modulating root development and absorption of nitrogen compounds.

Nitrogen in plants: from nutrition to the modulation of abiotic stress adaptation

Nitrogen is one of the most important nutrient for plant growth and development; it is strongly associated with a variety of abiotic stress responses. As sessile organisms, plants have evolved to develop efficient strategies to manage N to support growth when exposed to a diverse range of stressors. This review summarizes the recent progress in the field of plant nitrate (NO3-) and ammonium (NH4+) uptake, which are the two major forms of N that are absorbed by plants. We explore the intricate relationship between NO3-/NH4+ and abiotic stress responses in plants, focusing on stresses from nutrient deficiencies, unfavorable pH, ions, and drought. Although many molecular details remain unclear, research has revealed a number of core signaling regulators that are associated with N-mediated abiotic stress responses. An in-depth understanding and exploration of the molecular processes that underpin the interactions between N and abiotic stresses is useful in the design of effective strategies to improve crop growth, development, and productivity.

Integrated Analysis of miRNAs Associated With Sugarcane Responses to Low-Potassium Stress

Sugarcane is among the most important global crops and a key bioenergy source. Sugarcane production is restricted by limited levels of available soil potassium (K⁺). The ability of plants to respond to stressors can be regulated by a range of microRNAs (miRNAs). However, there have been few studies regarding the roles of miRNAs in the regulation of sugarcane responses to K⁺-deficiency. To understand how these non-coding RNAs may influence sugarcane responses to low-K⁺ stress, we conducted expression profiling of miRNAs in sugarcane roots under low-K⁺ conditions via high-throughput sequencing. This approach led to the identification of 324 and 42 known and novel miRNAs, respectively, of which 36 were found to be differentially expressed miRNAs (DEMs) under low-K⁺ conditions. These results also suggested that miR156-x/z and miR171-x are involved in these responses as potential regulators of lateral root formation and the ethylene signaling pathway, respectively. A total of 705 putative targets of these DEMs were further identified through bioinformatics predictions and degradome analyses, and GO and KEGG enrichment analyses revealed these target mRNAs to be enriched for catalytic activity, binding functions, metabolic processes, plant hormone signal transduction, and mitogen-activated protein kinase (MAPK) signaling. In summary, these data provide an overview of the roles of miRNAs in the regulation of sugarcane response to low-K⁺ conditions.

Morphophysiological and transcriptome analysis reveal that reprogramming of metabolism, phytohormones and root development pathways governs the potassium (K+) deficiency response in two contrasting chickpea cultivars

Potassium (K⁺) is an essential macronutrient for plant growth and development. K⁺ deficiency hampers important plant processes, such as enzyme activation, protein synthesis, photosynthesis and stomata movement. Molecular mechanism of K⁺ deficiency tolerance has been partly understood in model plants Arabidopsis, but its knowledge in legume crop chickpea is missing. Here, morphophysiological analysis revealed that among five high yielding desi chickpea cultivars, PUSA362 shows stunted plant growth, reduced primary root growth and low K⁺ content under K⁺ deficiency. In contrast, PUSA372 had negligible effect on these parameters suggesting that PUSA362 is K⁺ deficiency sensitive and PUSA372 is a K⁺ deficiency tolerant chickpea cultivar. RNA-seq based transcriptome analysis under K⁺ deficiency revealed a total of 820 differential expressed genes (DEG's) in PUSA362 and 682 DEGs in PUSA372. These DEGs belongs to different functional categories, such as plant metabolism, signal transduction components, transcription factors, ion/nutrient transporters, phytohormone biosynthesis and signalling, and root growth and development. RNA-seq expression of randomly selected 16 DEGs was validated by RT-qPCR. Out of 16 genes, 13 showed expression pattern similar to RNA-seq expression, that verified the RNA-seq expression data. Total 258 and 159 genes were exclusively up-regulated, and 386 and 347 genes were down-regulated, respectively in PUSA362 and PUSA372. 14 DEGs showed contrasting expression pattern as they were up-regulated in PUSA362 and down-regulated in PUSA372. These include somatic embryogenesis receptor-like kinase 1, thaumatin-like protein, ferric reduction oxidase 2 and transcription factor bHLH93. Nine genes which were down-regulated in PUSA362 found to be up-regulated in PUSA372, including glutathione S-transferase like, putative calmodulin-like 19, high affinity nitrate transporter 2.4 and ERF17-like protein. Some important carbohydrate metabolism related genes, like fructose-1,6-bisphosphatase and sucrose synthase, and root growth related Expansin gene were exclusively down-regulated, while an ethylene biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1) was up-regulated in PUSA362. Interplay of these and several other genes related to hormones (auxin, cytokinin, GA etc.), signal transduction components (like CBLs and CIPKs), ion transporters and transcription factors might underlie the contrasting response of two chickpea cultivars to K⁺ deficiency. In future, some of these key genes will be utilized in genetic engineering and breeding programs for developing chickpea cultivars with improved K⁺ use efficiency (KUE) and K⁺ deficiency tolerance traits.

Nitrogen form-mediated ethylene signal regulates root-to-shoot K+ translocation via NRT1.5

Nitrogen-potassium synergistic and antagonistic interactions are the typical case of nutrient interactions. However, the underlying mechanism for the integration of the external N form into K⁺ homeostasis remains unclear. Here, we show that opposite effects of NO₃^- and NH₄⁺ on root-shoot K⁺ translocation were due to differential regulation of an ethylene signalling pathway targeting the NRT1.5 transporter. NH₄⁺ upregulated the transcriptional activity of EIN3, but repressed the expression of NRT1.5. However, the addition of NO₃^- strongly suppressed the activity of EIN3, whereas its addition upregulated the expression of AtNRT1.5 and shoot K⁺ concentration. The 35S:EIN3/ein3eil1 plants, nrt1.5 mutants and nrt1.5/skor double mutants displayed a low K⁺ chlorosis phenotype, especially under NH₄⁺ conditions with low K⁺ supply. Ion content analyses indicate that root-to-shoot K⁺ translocation was significantly reduced in these mutants. A Y1H assay, an EMSA and a transient expression assay confirmed that AtEIN3 protein could directly bind to the promoter of NRT1.5 to repress its expression. Furthermore, grafted plants with the roots of 35S:EIN3 and ein3eil1/nrt1.5 mutants displayed marked leaf chlorosis with a low K⁺ concentration. Collectively, our findings reveal that the interaction between N form and K⁺ was achieved by modulating root-derived ethylene signals to regulate root-to-shoot K⁺ translocation via NRT1.5.

A spatial-temporal understanding of gene regulatory networks and NtARF-mediated regulation of potassium accumulation in tobacco

MAIN CONCLUSION

After tobacco topping, changes in the auxin content could affect K+ uptake by inhibiting the activity of K+ uptake-related genes through the NtARF genes, thus causing changes in K+ content. Tobacco (Nicotiana tabacum) is a valuable industrial and commercial crop, and the leaf is its primary product. Topping (removing apical buds) is a common agronomic practice that significantly improves the yield of tobacco leaves. Potassium (K+) plays an important physiological role in tobacco growth and leaf traits, including combustibility, aroma, and safety in cigarette products, and its levels are significantly decreased after topping. Here, to present global spatial-temporal gene expression profiles and gene regulatory networks of the core elements of K+ uptake, leaves and roots from topped and untopped plants at short- and long-term time points after topping were sampled for transcriptome analysis. We found that the wounding response was initiated in leaves in the early stages after topping. Then, in the long term, processes related to metabolism and transcription regulation, as well as ion binding and transport, were altered. The expression profiles showed that core elements of K+ uptake and xylem loading were drastically suppressed in roots after topping. Finally, transient expression experiments confirmed that changes in the auxin content could affect K+ uptake by inhibiting the activity of K+ uptake-related genes through the tobacco auxin response factor (NtARF) genes, thus causing changes in the K+ content. These results suggest that some ARFs could be selected as targets to enhance the expressions of K+ uptake transporters, leading to increment of K+ contents and improvement of leaf quality in tobacco breeding.

The MdABI5 transcription factor interacts with the MdNRT1.5/MdNPF7.3 promoter to fine-tune nitrate transport from roots to shoots in apple

Nitrate is a major nitrogen resource for plant growth and development and acts as both a crucial nutrient and a signaling molecule for plants; hence, understanding nitrate signaling is important for crop production. Abscisic acid (ABA) has been demonstrated to be involved in nitrate signaling, but the underlying mechanism is largely unknown in apple. In this study, we found that exogenous ABA inhibited the transport of nitrate from roots to shoots in apple, and the transcription of the nitrate transporter MdNRT1.5/MdNPF7.3 was noticeably reduced at the transcriptional level by ABA, which inhibited the transport of nitrate from roots to shoots. Then, it was found that the ABA-responsive transcription factor MdABI5 bound directly to the ABRE recognition site of the MdNRT1.5 promoter and suppressed its expression. Overexpression of MdABI5 inhibited ABA-mediated transport of nitrate from roots to shoots. Overall, these results demonstrate that MdABI5 regulates the transport of nitrate from roots to shoots partially by mediating the expression of MdNRT1.5, illuminating the molecular mechanism by which ABA regulates nitrate transport in apple.

Transcriptome and Metabolome Analyses Reveal Potential Salt Tolerance Mechanisms Contributing to Maintenance of Water Balance by the Halophytic Grass Puccinellia nuttalliana

Elevated soil salinity exacerbated by human activities and global climate change poses serious threats to plant survival. Although halophytes provide many important clues concerning salt tolerance in plants, some unanswered questions remain to be addressed, including the processes of water and solute transport regulation. We performed high-throughput RNA-sequencing in roots and metabolome characterizations in roots and leaves of Puccinellia nuttalliana halophytic grass subjected to 0 (control) and 150 mM NaCl. In RNAseq, a total of 31 Gb clean bases generated were de novo assembled into 941,894 transcripts. The PIP2;2 and HKT1;5 transcript levels increased in response to the NaCl treatment implying their roles in water and ion homeostasis. Several transcription factors, including WRKY39, DEK3, HY5, and ABF2, were also overexpressed in response to NaCl. The metabolomic analysis revealed that proline and dopamine significantly increased due to the upregulation of the pathway genes under salt stress, likely contributing to salt tolerance mechanisms. Several phosphatidylcholines significantly increased in roots suggesting that the alterations of membrane lipid composition may be an important strategy in P. nuttalliana for maintaining cellular homeostasis and membrane integrity under salt stress. In leaves, the TCA cycle was enriched suggesting enhanced energy metabolism to cope with salt stress. Other features contributing to the ability of P. nuttalliana to survive under high salinity conditions include salt secretion by the salt glands and enhanced cell wall lignification of the root cells. While most of the reported transcriptomic, metabolomics, and structural alterations may have consequences to water balance maintenance by plants under salinity stress, the key processes that need to be further addressed include the role of the changes in the aquaporin gene expression profiles in the earlier reported enhancement of the aquaporin-mediated root water transport.

Characterization of transcription factor MYB59 and expression profiling in response to low K+ and NO3- in indica rice (Oryza sativa L.)

Background

Nitrogen and potassium are crucial supplements for plant development and growth. Plants can detect potassium and nitrate ions in soils and in like way, they modify root-to-shoot transport of these ions to adjust the conveyance among roots and shoots. Transcription factor MYB59 plays essential roles in numerous physiological processes inclusive of hormone response, abiotic stress tolerance, plant development, and metabolic regulation. In this study, we retrieved 56 MYB59 proteins from different plant species. Multiple sequence alignment, phylogenetic tree, conserved motif, chromosomal localization, and cis-regulatory elements of the retrieved sequences were analyzed. Gene structure, protein 3D structure, and DNA binding of OsMYB59 indica were also predicted. Finally, we characterized OsMYB59 and its function under low K⁺/NO₃⁻ conditions in Oryza sativa subsp. indica.

Results

Data analysis showed that MYB59s from various groups separated in terms of conserved functional domains and gene structure, where members of genus Oryza clustered together. Plants showed reduced height and yellowish appearance when grown on K⁺ and NO₃⁻ deficient medium. Quantitative real-time PCR uncovered that the OsMYB59 reacted to abiotic stresses where its expression was increased in BRRI dhan56 but decreased in other varieties on K⁺ deficient medium. In addition, OsMYB59 transcript level increased on NO₃⁻ deficient medium.

Conclusions

Our results can help to explain the biological functions of indica rice MYB59 protein and gave a theoretical premise to additionally describe its biological roles in response to abiotic stresses particularly drought.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00248-6.

A potassium-sensing niche in Arabidopsis roots orchestrates signaling and adaptation responses to maintain nutrient homeostasis

Organismal homeostasis of the essential ion K⁺ requires sensing of its availability, efficient uptake, and defined distribution. Understanding plant K⁺ nutrition is essential to advance sustainable agriculture, but the mechanisms underlying K⁺ sensing and the orchestration of downstream responses have remained largely elusive. Here, we report where plants sense K⁺ deprivation and how this translates into spatially defined ROS signals to govern specific downstream responses. We define the organ-scale K⁺ pattern of roots and identify a postmeristematic K⁺-sensing niche (KSN) where rapid K⁺ decline and Ca²⁺ signals coincide. Moreover, we outline a bifurcating low-K⁺-signaling axis of CIF peptide-activated SGN3-LKS4/SGN1 receptor complexes that convey low-K⁺-triggered phosphorylation of the NADPH oxidases RBOHC, RBOHD, and RBOHF. The resulting ROS signals simultaneously convey HAK5 K⁺ uptake-transporter induction and accelerated Casparian strip maturation. Collectively, these mechanisms synchronize developmental differentiation and transcriptome reprogramming for maintaining K⁺ homeostasis and optimizing nutrient foraging by roots.

MYB59 transcription factor behaves differently in metallicolous and non-metallicolous populations of Arabidopsis halleri

In Arabidopsis thaliana (L.) Heynh., MYB59 transcription factor participates in regulating Ca homeostasis and signal transduction and is induced by Cd excess. To investigate its role in the facultative metallophyte Arabidopsis halleri ssp. halleri (L.) O'Kane and Al-Shehbaz, MYB59 expression was investigated under Cd treatment or Ca depletion in three populations belonging to distinct phylogeographic units (metallicolous PL22 and I16 and non-metallicolous I29), and compared with the expression in A. thaliana. In control conditions, MYB59 transcription in A. thaliana and the non-metallicolous population I29 follow a comparable trend with higher expression in roots than shoots, whereas in metallicolous populations I16 and PL22 its expression is similar in roots and shoots, suggesting a convergent evolution associated with adaptation to metalliferous environments. After 6 h of Ca depletion, MYB59 transcript levels were very high in I16 and PL22 populations, indicating that the adaptation to metalliferous environments requires tightly regulated Ca homeostasis and signalling. Cd treatment caused variability in MYB59 expression. In I29, MYB59 expression, as in A. thaliana, is likely associated to stress response, whereas its modulation in the two metallicolous populations reflects the different strategies for Cd tolerance and accumulation. In conclusion, MYB59 regulation in A. halleri is part of the network linking mineral nutrition and Cd tolerance/accumulation.