ZmNRT1.1B (ZmNPF6.6) determines nitrogen use efficiency via regulation of nitrate transport and assimilation in maize
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA945327 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23876200_1.fastq.gz | Fastqsanger.gz | |||
| SRR23876200_2.fastq.gz | Fastqsanger.gz | |||
| SRR23876201_1.fastq.gz | Fastqsanger.gz | |||
| SRR23876201_2.fastq.gz | Fastqsanger.gz | |||
| SRR23876202_1.fastq.gz | Fastqsanger.gz |
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Project description:Nitrate (NO3-) is crucial for optimal plant growth and development and often limits crop productivity at the low availability. In comparison with model plant Arabidopsis, the molecular mechanisms underlying NO3- acquisition and utilization remain largely unclear in maize. In particular, only a few genes have been exploited to improve nitrogen use efficiency (NUE). Here, we demonstrated that NO3--inducible ZmNRT1.1B (ZmNPF6.6) positively regulated NO3--dependent growth and NUE in maize. We showed that the tandem duplicated proteoform ZmNRT1.1C is irrelevant to maize seedling growth under nitrate supply, however, loss-of-function of ZmNRT1.1B significantly weakened plant growth under adequate NO3- supply in both hydroponic and field conditions. 15N-labeled NO3- absorption assay indicated that ZmNRT1.1B mediated high-affinity NO3--transport and root-to-shoot NO3- translocation. Furthermore, upon NO3- supply, ZmNRT1.1B promotes cytoplasmic-to-nuclear shuttling of ZmNLP3.1 (ZmNLP8), which co-regulates the expression of genes involved in NO3- response, cytokinin biosynthesis and carbon metabolism. Remarkably, overexpression of ZmNRT1.1B in modern maize hybrids improved grain yield under nitrogen (N) limiting fields. Taken together, our study revealed a crucial role of ZmNRT1.1B in high-affinity NO3- transport and signaling and offers valuable genetic resource for breeding nitrogen use efficient high-yield cultivars.
2023-04-25 | GSE227472 | GEO
Project description:The goal of this work was to investigate the influence of low red to far-red (R:FR) signals generated by a biological weedy and an artificial source of far-red light on the nitrate assimilation pathway in maize. In the absence of direct resource competition, far-red light reflected from neighboring weeds compromises light quality (red to far-red ratio; R/FR) and causes a wide range of morphological and physiological responses at early growth stages of crop plants. This study has investigated the effects of low R/FR light signals on nitrate assimilation in maize seedlings. The transcript levels of genes, metabolites, and activities of enzyme in the nitrate assimilation pathway under a biological and a simulated low R:FR light environment were compared with a high R:FR control environment. Low R:FR signals stimulated nitrate accumulation in maize leaves, which did not appear to result from the upregulation of nitrate transporter genes. A significant reduction in ferredoxin-dependent glutamine:2-oxoglutarate aminotransferase activity appears to play a major role in nitrate accumulation under low R:FR light environments, while activities of other enzymes of the nitrate assimilation pathway remain unchanged.
2022-09-27 | GSE213949 | GEO
Project description:Nitrate (NO3 - ) is crucial for optimal plant growth and development and often limits crop productivity under low availability. In comparison with model plant Arabidopsis, the molecular mechanisms underlying NO3 - acquisition and utilization remain largely unclear in maize. In particular, only a few genes have been exploited to improve nitrogen use efficiency (NUE). Here, we demonstrated that NO3 - -inducible ZmNRT1.1B (ZmNPF6.6) positively regulated NO3 - -dependent growth and NUE in maize. We showed that the tandem duplicated proteoform ZmNRT1.1C is irrelevant to maize seedling growth under NO3 - supply; however, the loss of function of ZmNRT1.1B significantly weakened plant growth under adequate NO3 - supply under both hydroponic and field conditions. The 15 N-labelled NO3 - absorption assay indicated that ZmNRT1.1B mediated the high-affinity NO3 - -transport and root-to-shoot NO3 - translocation. Transcriptome analysis further showed, upon NO3 - supply, ZmNRT1.1B promotes cytoplasmic-to-nuclear shuttling of ZmNLP3.1 (ZmNLP8), which co-regulates the expression of genes involved in NO3 - response, cytokinin biosynthesis and carbon metabolism. Remarkably, overexpression of ZmNRT1.1B in modern maize hybrids improved grain yield under N-limiting fields. Taken together, our study revealed a crucial role of ZmNRT1.1B in high-affinity NO3 - transport and signalling and offers valuable genetic resource for breeding N use efficient high-yield cultivars.
| S-EPMC10826987 | biostudies-literature
Project description:Nitrate is the limiting nitrogen nutrient enabling photosynthetic plants to support the conversion of inorganic elements to organic biomass, which sustains all lives. Plants evolved multifaceted nitrate responses to modulate global gene expression, metabolism and developmental programs. However, primary nitrate signaling mechanisms remained elusive. Using an ultrasensitive Ca2+ biosensor, unique nitrate-induced Ca2+ signaling was illuminated in Arabidopsis cells and plants. Integrative functional genomic screens, chemical genetics, genome-wide transcript sequencing, and analyses of nitrate-associated traits uncovered the surprising roles of Ca2+ sensor protein kinases (CPKs) in orchestrating diverse primary and long-term nitrate responses. Nitrate specifies CPK signaling to reprogram transcriptome and govern N-assimilation, metabolism, transport, hormones, shoot growth, and root system architecture. CPKs may be targeted to enhance nitrogen-use-efficiency, reduce fertilizer demands, and alleviate ecosystem pollution.
2017-05-19 | GSE73437 | GEO
Project description:gnp3-b4_nitrogen_starvation - nitrogen starvation and re-supply - What are the transcriptomic short- and long-term plant responses to nitrogen starvation and nitrogen re-supply? - WS Arabidopsis ecotype were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 and 24 hours (T+1, T+24). Keywords: time course
2007-06-20 | GSE8031 | GEO
Project description:Plants take up nitrate in soils and utilize it both for nitrogen assimilation and as a signaling molecule. Thus, an essential role of nitrate in plants is triggering changes in gene expression patterns, including immediate induction of the expression of genes involved in nitrate transport and assimilation as well as several transcription factor genes and genes related with carbon metabolism and cytokinin biosynthesis and response. Recently we identified NIN-like proteins (NLPs) as transcription factors governing nitrate-inducible gene expression in Arabidopsis. Because of their similar DNA-binding property, nine NLP proteins may play redundant roles in controlling nitrate-regulated gene expression in Arabidopsis. The physiological roles of NLPs were therefore assessed by generating transgenic Arabidopsis plants expressing NLP6 fused to the transcriptional repression domain of SUPERMAN (SUPRD), which has an ability to convert transcriptional activators into transcriptional repressors. Our transcriptome analysis revealed that levels of nitrate-inducible expression of nitrate transporter genes (NRT1.1 and NRT2.1), nitrate reduction enzyme genes (NIA1, NIA2 and NIR1), the genes associated with ammonium assimilation (GLT1 for glutamine-2-oxoglutarate aminotransferase and ASN2 for asparagine synthetase), LBD37-39 transcription factor genes and genes encoding homologs of rice nitrate-inducible NIGT1 transcriptional repressor, were reduced in the NLP6-SUPRD lines. Furthermore, levels of nitrate-inducible expression of the genes associated with the oxidative pentose phosphate pathway (G6PD2 and G6PD3 for glucose-6-phosphate dehydrogenases, and 6-phosphogluconate dehydrogenase genes), cytokinin biosynthesis (IPT3) and signal transduction (A-type ARR genes), a gene encoding a Ser/Thr protein kinase associated with a calcineurin B–like calcium sensor (CIPK3) were also found to be largely decreased by reductions in NLP activity. Because induction folds by nitrate and reduction folds by decreases in the NLP activity were well proportional, the NLP activity appeared to be responsible for most of nitrate responsiveness of the genes whose expression occurs immediately after nitrate treatment.
2014-01-07 | GSE53852 | GEO
Project description:Purpose: RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. Methods: mRNA profiles of Aureococcus anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed by aligning to reference genome and transcript using SOAPaligner/SOAP2 (version 2.21). Results: Deconvolution and filtering of raw reads yielded a mean of 6,938,798 reads (range: 6,539,842 to 7,242,083 reads) per individual RNA-seq library (Table 1). Subsequent alignment of the clean reads to the A. anophagefferens reference genome yielded a mean of 5,852,408 reads (84.3%) for each sample that mapped to at least one location in the A. anophagefferens genome. However, of these mapped reads, only 47.4 to 50.9% of the total reads were mapped to the reference transcript for each sample (Table 2). In A. anophagefferens grown on three different N sources, 9148 to 9526 genes were detected for each sample. A comparison of gene expression among the three N sources was performed. 322 differentially expressed genes were detected between nitrate-grown and urea-grown cells, 237 between nitrate-grown and mixture N-grown cells and 29 between urea-grown and mixture N-grown cells. Fewer differentially expressed genes between urea-grown and mixture N-grown cells were identified, which further suggested the preferred utilization of cells for urea in media with mixture N. For nitrogen-limited and recovery experiments, 707 genes were up-regulated significantly, and 766 were down-regulated significantly in N-depleted cells relative to N-replete cells. N-depleted cells exhibited a broad transcriptional response to nitrogen re-addition, with 681 genes up-regulated and 874 genes down-regulated in urea recovery cells, and 312 genes up-regulated and 688 genes down-regulated in nitrate recovery cells. Conclusions: We noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid, nucleotide and aminosugar transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. Seven mRNA samples for Aureococcus anophagefferens were sequencd using Illumina HiSeqTM 2000, including three samples that was grown on urea, nitrate, and a mixture of urea and nitrate, and four samples that was under N-replete, limited and recovery conditions
2015-05-14 | E-GEOD-60576 | biostudies-arrayexpress
Project description:Purpose: RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. Methods: mRNA profiles of Aureococcus anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed by aligning to reference genome and transcript using SOAPaligner/SOAP2 (version 2.21). Results: Deconvolution and filtering of raw reads yielded a mean of 6,938,798 reads (range: 6,539,842 to 7,242,083 reads) per individual RNA-seq library (Table 1). Subsequent alignment of the clean reads to the A. anophagefferens reference genome yielded a mean of 5,852,408 reads (84.3%) for each sample that mapped to at least one location in the A. anophagefferens genome. However, of these mapped reads, only 47.4 to 50.9% of the total reads were mapped to the reference transcript for each sample (Table 2). In A. anophagefferens grown on three different N sources, 9148 to 9526 genes were detected for each sample. A comparison of gene expression among the three N sources was performed. 322 differentially expressed genes were detected between nitrate-grown and urea-grown cells, 237 between nitrate-grown and mixture N-grown cells and 29 between urea-grown and mixture N-grown cells. Fewer differentially expressed genes between urea-grown and mixture N-grown cells were identified, which further suggested the preferred utilization of cells for urea in media with mixture N. For nitrogen-limited and recovery experiments, 707 genes were up-regulated significantly, and 766 were down-regulated significantly in N-depleted cells relative to N-replete cells. N-depleted cells exhibited a broad transcriptional response to nitrogen re-addition, with 681 genes up-regulated and 874 genes down-regulated in urea recovery cells, and 312 genes up-regulated and 688 genes down-regulated in nitrate recovery cells. Conclusions: We noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid, nucleotide and aminosugar transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source.
2015-05-14 | GSE60576 | GEO
Project description:Identification of glnR-dependent regulation of nitrate assimilation Keywords: genetic modification
2009-04-03 | GSE13246 | GEO
Project description:Nitrogen (N) is an essential macronutrient for agricultural production, and its excessive use causes not only economic but also environmental damage. However, improving nitrogen use efficiency (NUE) remains a complex task for achieving more productive crops under conditions of limited nitrogen availability. To the best of our knowledge, this is the first study aiming to integrate the morphophysiological responses and proteomic profiles of leaves and roots of popcorn (Zea mays everta). For this, two inbred lines contrasting for NUE, i.e., P2 (high NUE) and L80 (low NUE), were cultivated under high (100% of N supply) and low (10% of N supply) nitrogen conditions. Morphological and physiological traiits such as photochemical quenching (qP), non-photochemical quenching (NPQ), quantum yield of photosystem II (ΦPSII), and potential photosynthesis (Apot) were evaluated. P2 showed more pronounced vegetative growth under low N, as well as higher values of qP, NPQ, and ΦPSII. Comparative proteomic analysis of the leaves identified 215 differentially accumulated proteins (DAPs) in P2 and 168 DAPs in L80, while in roots, 127 DAPs were observed in P2 and 172 in L80. In leaves, DAPs involved in the response to oxidative stress, energy metabolism, and photosynthesis represented the main differences between P2 and L80. In roots, DAPs involved in nitrate transport, ammonium assimilation, and amino acid metabolism seem to have contributed to the improved NUE in P2. This study provides valuable insights into the molecular mechanisms underlying NUE and opens avenues for molecular breeding aimed at selecting superior genotypes for the development of a more sustainable agriculture.
2025-03-11 | PXD048990 | Pride