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

Lhamo, Dhondup; Luan, Sheng

doi:10.3389/fpls.2021.689545

Cited by 11 publications

(10 citation statements)

References 244 publications

(434 reference statements)

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“…4B ; Contreras-López et al 2022 ). This is in line with previous studies that identified the cell type specificity of nitrate transporters in the epidermis ( Tegeder and Masclaux-Daubresse 2018 ; Wang et al 2018 ; Lhamo and Luan 2021 ; Muratore et al 2021 ). At later times, expression of genes involved in “nitrate assimilation” are enriched from inner cell types toward the epidermis ( Fig.…”

Section: The Dynamics Of Nitrogen Responses In Specific Cell Typessupporting

confidence: 92%

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

Shanks,

Rothkegel,

Brooks

et al. 2024

The Plant Cell

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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.

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Section: The Dynamics Of Nitrogen Responses In Specific Cell Typessupporting

confidence: 92%

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

Shanks,

Rothkegel,

Brooks

et al. 2024

The Plant Cell

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show abstract

“…BnaA10g19700D (AtXTH5) encoding endoxyloglucan transferase has been reported to regulate root cap during nitrogen stress [ 66 ]. Another important gene, BnaC07g30400D (AtSLAH3), plays a potential role in nitrogen uptake and assimilation during nitrogen-deprived conditions [ 67 , 68 , 69 ].…”

Section: Discussionmentioning

confidence: 99%

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

Ahmad

Ibrahim

et al. 2022

IJMS

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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.

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“…We also identified MEKK19, and MPK19 as potential interactors, though the function of these kinases is unknown. Several transporters were also identified as potential ILK1 interactors including the KUP5 potassium transporter which is closely related to HAK5, and is expressed across diverse root cell types ( Lhamo and Luan, 2021 ). This indicates that ILK1 can interact with a wide range of protein types in vitro , supporting the notion that additional ILK1-protein interactions beyond the CML9 and HAK5 proteins may exist in plant cells.…”

Section: Resultsmentioning

confidence: 99%

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

Brauer

Ahsan²,

Popescu³

et al. 2022

Front. Plant Sci.

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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.

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

Cited by 11 publications

References 244 publications

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

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

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

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

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