Genome-wide identification of nitrate transporter genes from Spirodela polyrhiza and characterization of SpNRT1.1 function in plant development

Dong, Tiantian; Wang, Jin; Zuo, Kaijing

doi:10.3389/fpls.2022.945470

Cited by 2 publications

(2 citation statements)

References 56 publications

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“…Meanwhile, NRT1.5 (BraA05g023200.3C), NRT1.8 (BraA03g049670.3C), NPF3.1(BraA07g030700.3C), and NPF6.4 (BraA05g025490.3C) were highly expressed in L14. Our findings are in accordance with previous studies in B. rapa, Poncirus trifoliata, and Spirodela polyrhiza [39,44,45]. Hence, we assumed these genes could provide valuable allelic variations for the enhancement of nutrient use efficiency (NUE) in Chinese cabbage.…”

Section: Discussionsupporting

confidence: 92%

Genome-Wide Identification of the NRT1 Family Members and Their Expression under Low-Nitrate Conditions in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Zhang,

Ritonga,

Zhang

et al. 2023

Plants

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Nitrate transporters (NRTs) actively take up and transform nitrate (N) to form a large family with many members and distinct functions in plant growth and development. However, few studies have identified them in the context of low nitrate concentrations in Chinese cabbage (Brassica rapa L. ssp. Pekinensis), an important vegetable in China. This study focuses on the identification and analysis of the nitrate transporter 1 (NRT1) gene family as well as various aspects, including its phylogenic distribution, chromosomal position, gene structure, conserved motifs, and duplication pattern. Using bioinformatics methods, we identified and analyzed 84 BrNRT1 genes distributed on ten chromosomes. Furthermore, we conducted an analysis of the expression profile of the NRT1 gene in various tissues of Chinese cabbage exposed to varying nitrate concentrations. A phylogenetic analysis revealed that BrNRT1s members are distributed in six distinct groups. Based on an analysis of gene structure and conserved motifs, it can be inferred that BrNRT1 exhibits a generally conserved structural pattern. The promoters of BrNRT1 were discovered to contain moosefs (MFS) elements, suggesting their potential role in the regulation of NO3− transport across the cell membrane in Chinese cabbage. A transcriptome study and a subsequent RT-qPCR analysis revealed that the expression patterns of some BrNRT1 genes were distinct to specific tissues. This observation implies these genes may contribute to nitrate uptake and transport in various tissues or organs. The results offer fundamental insights into investigating the NRT1 gene family in Chinese cabbage. These results provide basic information for future research on the functional characterization of NRT1 genes in Chinese cabbage and the elucidation of the molecular mechanisms underlying low nitrogen tolerance in Chinese cabbage.

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Section: Discussionsupporting

confidence: 92%

Genome-Wide Identification of the NRT1 Family Members and Their Expression under Low-Nitrate Conditions in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Zhang,

Ritonga,

Zhang

et al. 2023

Plants

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“…Genome-wide identification of NPF genes have been extensively studied in diverse plant species, including Arabidopsis ( Léran et al., 2014 ), rice ( Yang et al., 2020a ), Populus tomentosa ( Zhao et al., 2021 ), Spirodela polyrhiza ( Lv et al., 2022 ) and Triticum aestivum ( Kumar et al., 2022 ). However, there has been little information about NPF family in the barren tolerant species Setaria , which greatly limits our understanding of the molecular mechanisms underlying high NUE in this species.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria

et al. 2022

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IntroductionNitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N.MethodsBioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2.ResultsWe identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins with NO3− were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs- NO3− binding energy ranged from -3.8 to -2.7 kcal/mol.DiscussionTaken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.

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Genome-wide identification of nitrate transporter genes from Spirodela polyrhiza and characterization of SpNRT1.1 function in plant development

Cited by 2 publications

References 56 publications

Genome-Wide Identification of the NRT1 Family Members and Their Expression under Low-Nitrate Conditions in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Genome-Wide Identification of the NRT1 Family Members and Their Expression under Low-Nitrate Conditions in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria

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