Potential Networks of Nitrogen-Phosphorus-Potassium Channels and Transporters in Arabidopsis Roots at a Single Cell Resolution

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.

Nitrogen sensing and regulatory networks: it's about time and space

A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.

Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants

Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.

Five Post-Translational Modification Residues of CmPT2 Play Key Roles in Yeast and Rice

Chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the largest cut flowers in the world. Phosphate transporter Pht1 family member CmPht1;2 protein (CmPT2) plays an important role in response to low-phosphate (LP) stress in chrysanthemum. Post-translational modification (PTM) can modulate the function of proteins in multiple ways. Here, we used yeast and rice systems to study the role of putative PTM in CmPT2 by determining the effect of mutation of key amino acid residues of putative glycosylation, phosphorylation, and myristoylation sites. We chose nine amino acid residues in the putative PTM sites and mutated them to alanine (A) (Cmphts). CmPT2 recovered the growth of yeast strain MB192 under LP conditions. However, G84A, G222A, T239A, Y242A, and N422A mutants could not grow normally under LP conditions. Analysis of phosphorus absorption kinetics showed that the Km of CmPT2 was 65.7 μM. Among the nine Cmphts, the expression of five with larger Km (124.4-397.5 μM) than CmPT2 was further evaluated in rice. Overexpression of CmPT2-OE increased plant height, effective panicle numbers, branch numbers, and yield compared with that of wild type 'Wuyunjing No. 7' (W7). Overexpression of Cmphts-OE led to decreased plant height and effective panicle numbers compared with that of the CmPT2-OE strain. The Pi content in roots of CmPT2-OE was higher than that of the W7 under both high (normal) phosphate (HP) and LP conditions. However, the Pi content in the leaves and roots was significantly lower in the N422A-OE strain than in the CmPT2-OE strain under both HP and LP conditions. Under LP conditions, the phosphorus starvation response (PSR) genes in CmPT2-OE were inhibited at the transcription level. The expression patterns of phosphorus-related genes in T239A, Y242A, and N422A-OE under LP conditions were different from those of CmPT2-OE. In conclusion, these five post-translational modification residues of CmPT2 play key roles in modulating the function of CmPT2. This work boosters our understanding of the function of phosphate transporters and provides genetic resources for improving the efficiency of phosphorus utilization in crop plants.

Short-term trade-offs of organic matter management strategies for smallholder farms

Organic matter management (OMM) strategies such as farmyard manure (FYM) application, legume integration, crop residue incorporation, and alley cropping are recognized for improving soil fertility and crop productivity. However, studies on yield and economics of a combination of such strategies on smallholder farms are generally scarce, yet an understanding of such can enhance adoption. This study analyzed the yield and gross margins of crops grown with OMM strategies in comparison to those grown under inorganic fertilizer application on smallholder farms. Field experiments with five treatments over two short rainy (SR) and two long rainy (LR) seasons were conducted from January 2018 to February 2020 on 10 smallholder farms. The treatments (T) included T1 (control): the inorganic fertilizer application strategy that involved maize monocrop with 50 kg/ha Diammonium phosphate (DAP) application and the OMM strategies (T2-T5). T2: cowpea-maize-bean-maize rotation; T3: cowpea-maize-bean-maize rotation + 2.5 tons/ha FYM; T4: Faidherbia albida alleys + cowpea-maize-bean-maize rotation; and T5: Faidherbia albida alleys + cowpea-maize-bean-maize rotation + 2.5 tons/ha FYM. The maize in T3-T5 was intercropped with Mucuna pruriens. The results indicate that the grain and residue yields in LR were not significantly different among all treatments. The total variable costs, which included monetarized labor and annualized capital costs for the establishment of F. albida were significantly higher under T1 than in T2-T5 during LR2018 and not significantly different from what was observed under T3-T5 in LR2019. The accumulated revenues and gross margins for the four seasons were not significantly different between T1 and the OMM strategies. We conclude that the integration of OMM strategies can give gross margins similar to the 50 kg/ha DAP application. Further, based on the price sensitivity analysis, we conclude that the smallholder farmers could adopt T3 and T4 as the gross margins under these treatments are less affected by grain price fluctuations than in T1, T2, and T5. Since the smallholder farmers can access the planting materials, we recommend the adoption of T3 and T4 on smallholder farms.

Back From the Dead: The Atypical Kinase Activity of a Pseudokinase Regulator of Cation Fluxes During Inducible Immunity

Pseudokinases are thought to lack phosphotransfer activity due to altered canonical catalytic residues within their kinase domain. However, a subset of pseudokinases maintain activity through atypical phosphotransfer mechanisms. The Arabidopsis ILK1 is a pseudokinase from the Raf-like MAP3K family and is the only known plant pseudokinase with confirmed protein kinase activity. ILK1 activity promotes disease resistance and molecular pattern-induced root growth inhibition through its stabilization of the HAK5 potassium transporter with the calmodulin-like protein CML9. ILK1 also has a kinase-independent function in salt stress suggesting that it interacts with additional proteins. We determined that members of the ILK subfamily are the sole pseudokinases within the Raf-like MAP3K family and identified 179 novel putative ILK1 protein interactors. We also identified 70 novel peptide targets for ILK1, the majority of which were phosphorylated in the presence of Mn²⁺ instead of Mg²⁺ in line with modifications in ILK1's DFG cofactor binding domain. Overall, the ILK1-targeted or interacting proteins included diverse protein types including transporters (HAK5, STP1), protein kinases (MEKK1, MEKK3), and a cytokinin receptor (AHK2). The expression of 31 genes encoding putative ILK1-interacting or phosphorylated proteins, including AHK2, were altered in the root and shoot in response to molecular patterns suggesting a role for these genes in immunity. We describe a potential role for ILK1 interactors in the context of cation-dependent immune signaling, highlighting the importance of K⁺ in MAMP responses. This work further supports the notion that ILK1 is an atypical kinase with an unusual cofactor dependence that may interact with multiple proteins in the cell.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.