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      Genome wide analysis of NLP transcription factors reveals their role in nitrogen stress tolerance of rice

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          Abstract

          The NIN-LIKE PROTEIN (NLP) family of transcription factors were identified as nitrate-responsive cis-element (NRE)-binding proteins, which function as transcriptional activators in the nitrate-regulated expression of downstream genes. This study was aimed at genome-wide analysis of NLP gene family in rice and the expression profiling of NLPs in response to nitrogen (N) supply and deficiency in rice genotypes with contrasting N use efficiency (NUE). Based on in silico analysis, 6 NLP genes (including alternative splice forms 11 NLPs) were identified from rice. Expression of NLPs was promoted by nitrate supply as well as N deficiency ( NLP1, NLP3, NLP4 and NLP5). Four rice genotypes APO (high NUE under sufficient N), IR83929-B-B-291-3-1-1 (IR-3-1-1), Nerica-L-42 (NL-42) (High NUE at low N), and Pusa Basmati 1 (PB1, low NUE) to correlate traits governing NUE and expression of NLPs. Analysis of rate of nitrate uptake and expression of N assimilatory and uptake genes established that IR-3-1-1 has high uptake and assimilation efficiency, translating into high NUE, whereas PB1 is efficient in uptake only when N availability is high. Along with the transcriptional upregulation of NLPs, genotype IR-3-1-1, displayed highest expression of OsNRT1.1B gene, the closest rice homologue of nitrate transceptor AtNRT1.1 and plays major role in nitrate uptake, translocation and signaling in rice. The results showed that high NUE rice genotypes has both high Nitrogen uptake efficiency (NUpE) and Nitrogen utilization efficiency (NUtE), resulting from the effective and coordinated signal transduction network involving the rice homologue of nitrate transceptor OsNRT1.1B, the probable primary nitrate response (PNR) regulator Os NLP1 and the master response regulator OsNLP3, a homologue of AtNLP6 /7.

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          Most cited references31

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          CHL1 functions as a nitrate sensor in plants.

          Ions serve as essential nutrients in higher plants and can also act as signaling molecules. Little is known about how plants sense changes in soil nutrient concentrations. Previous studies showed that T101-phosphorylated CHL1 is a high-affinity nitrate transporter, whereas T101-dephosphorylated CHL1 is a low-affinity transporter. In this study, analysis of an uptake- and sensing-decoupled mutant showed that the nitrate transporter CHL1 functions as a nitrate sensor. Primary nitrate responses in CHL1T101D and CHLT101A transgenic plants showed that phosphorylated and dephosphorylated CHL1 lead to a low- and high-level response, respectively. In vitro and in vivo studies showed that, in response to low nitrate concentrations, protein kinase CIPK23 can phosphorylate T101 of CHL1 to maintain a low-level primary response. Thus, CHL1 uses dual-affinity binding and a phosphorylation switch to sense a wide range of nitrate concentrations in the soil, thereby functioning as an ion sensor in higher plants. For a video summary of this article, see the PaperFlick file with the Supplemental Data available online.
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            Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.

            Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.
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              Discovery of nitrate–CPK–NLP signalling in central nutrient–growth networks

              In response to nitrate, Ca2+-sensor protein kinases (CPKs) act as master regulators to coordinate downstream signalling responses that are essential for shoot growth and root establishment in Arabidopsis.
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                Author and article information

                Contributors
                lekshmyrnair@gmail.com
                viswa_iari@hotmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                10 June 2020
                10 June 2020
                2020
                : 10
                : 9368
                Affiliations
                [1 ]ISNI 0000 0001 2172 0814, GRID grid.418196.3, Division of Plant Physiology, , ICAR-Indian Agricultural Research Institute, ; New Delhi, India
                [2 ]ISNI 0000 0001 2172 0814, GRID grid.418196.3, Division of Genetics, , ICAR-Indian Agricultural Research Institute, ; New Delhi, India
                [3 ]IRRI South Asia Regional Centre (ISARC), Varanasi, 221006 Uttar Pradesh India
                [4 ]Division of Crop Research, ICAR Research Complex For Eastern Region, Patna, Bihar India
                Article
                66338
                10.1038/s41598-020-66338-6
                7287097
                32523127
                1d870da7-3e4f-4a43-b3c3-06e51e85f9d8
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 19 December 2019
                : 14 May 2020
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                © The Author(s) 2020

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                plant sciences,plant physiology
                Uncategorized
                plant sciences, plant physiology

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