Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana

Asim, Muhammad; Ullah, Zia; Xu, Fangzheng; An, Lulu; Aluko, Oluwaseun Olayemi; Wang, Qian; Liu, Haobao

doi:10.3390/genes11060633

Cited by 48 publications

(26 citation statements)

References 132 publications

(259 reference statements)

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“…The strategy of European beech for dealing with high loads of inorganic N availability was transcriptional upregulation of genes involved in N uptake and assimilation, as observed in Arabidopsis (51),a non-mycorrhizal species. The transcription patterns in response to nitrate and ammonium were clearly distinguishable, in agreement with other studies that documented nitrate- and ammonium-specific effects on gene regulation, signaling and lateral root growth (95–100). Notably, transcripts belonging to putative NRTs and to enzymes (NR, NiR, GS) were significantly upregulated in the nitrate treatment encompassing the suite of reactions required for NO 3 - reduction and incorporation into amino acids (Fig.…”

Section: Discussionsupporting

confidence: 90%

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provide Insight into N Uptake from Forest Soil

Perez

Janz

Schneider

et al. 2021

Preprint

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Mineral nitrogen (N) is a major nutrient showing strong fluctuations in the environment due to anthropogenic activities. Acquisition and translocation of N to forest trees is achieved by highly diverse ectomycorrhizal fungi (EMF) living in symbioses with their host roots. Here, we examined colonized root tips to characterize the entire root-associated fungal community by DNA metabarcoding-Illumina sequencing of the fungal ITS2 molecular marker and used RNA sequencing to target metabolically active fungi and the plant transcriptome after N application. The study was conducted with beech (Fagus sylvatica L), a dominant tree species in central Europe, grown in native forest soil. We demonstrate strong enrichment of 15N from nitrate or ammonium in the ectomycorrhizal roots by stable isotope labeling. The relative abundance of the EMF members in the fungal community was correlated with their transcriptional abundances. The fungal metatranscriptome covered KEGG and KOG categories similar to model fungi and did not reveal significant changes related to N metabolization but species-specific transcription patterns, supporting trait stability. In contrast to the resistance of the fungal metatranscriptome, the transcriptome of the host exhibited dedicated nitrate- or ammonium-responsive changes with upregulation of transporters and enzymes required for nitrate reduction and drastic enhancement of glutamine synthetase transcript levels, indicating channeling of ammonium into the pathway for plant protein biosynthesis. Our results support that self-composed fungal communities associated with tree roots buffer nutritional signals in their own metabolism but do not shield plants from high environmental N.

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Section: Discussionsupporting

confidence: 90%

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provide Insight into N Uptake from Forest Soil

Perez

Janz

Schneider

et al. 2021

Preprint

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“…The root system architecture (RSA) is a highly modulated morphological system, affected by variations in the availability of nutrients [ 79 , 80 , 81 ], such as N [ 82 ]. Rice roots demonstrated a typical monocotyledon secondary homorhizic RSA; thus, PRs, crown roots (CRs), and LRs form in the 14-day-old rice seedlings [ 83 , 84 , 85 , 86 , 87 ].…”

Section: Discussionmentioning

confidence: 99%

“…PR and LR elongation can be induced by a moderate level of N reduction, but inhibited by severe N limitation [ 79 , 84 , 89 , 91 , 92 ]. Here, LR elongation was not noted in LY9348; therefore, LY9348 may demonstrate a different LR modulation.…”

Section: Discussionmentioning

confidence: 99%

Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)

Liang

Yuan

et al. 2021

IJMS

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Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH4NO3 (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH4NO3 (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.

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“…Nitrate availability strongly affects root development [35][36][37][38]. Previous works on maize seedlings evidence the role played by nitric oxide (NO) produced by nitrate reductase (NR) in inducing the root apex to elongate soon after nitrate provision [15][16][17].…”

Section: Discussionmentioning

confidence: 99%

Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms

Ravazzolo

Trevisan

Iori

et al. 2021

IJMS

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Maize root responds to nitrate by modulating its development through the coordinated action of many interacting players. Nitric oxide is produced in primary root early after the nitrate provision, thus inducing root elongation. In this study, RNA sequencing was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency on, or independency of, nitric oxide, thus discriminating the signaling pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to gain further information and the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots. Our results led us to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, shared and specific features for the six clusters were identified, allowing us to determine the overall root response to nitrate according to its dependency on nitric oxide.

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Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana

Cited by 48 publications

References 132 publications

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provide Insight into N Uptake from Forest Soil

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provide Insight into N Uptake from Forest Soil

Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)

Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms

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