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

Ting Liang,Lu Fu,Menghan Zhu,Xianting Wu,Zhongli Hu,Zhengqing Yuan,Huanran Yuan,Renshan Zhu,Xiaoyun Luo,Wuwu Xu

doi:10.3390/ijms22147674

Abstract

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.

Highlights

Rice (Oryza sativa L.) is a main crop in many countries worldwide [1], including China
Honglian-type cytoplasmic sterility (CMS) is one of the three major CMS for three-line hybrid rice generation, and the hybrid rice variety LY9348 produced by Honglian-type male sterile line Longhong4A demonstrates remarkable agricultural characteristics, such as high yield, broad adaptability, disease resistance, insect resistance, high temperature tolerance, and high nitrogen use efficiency (NUE) [5,6]
primary root (PR) elongation was the lowest with the 0N and 4N treatments (Figure 1A,C), which indicated that PR-inhibited phenotypes were identified under severe N deficiency (0N) and under oversupplied N (4N) conditions in LY9348

Summary

Introduction

Rice (Oryza sativa L.) is a main crop in many countries worldwide [1], including China. It contributes to 43.7% and 36.9% of the total grain output in China and worldwide, respectively [2]. In China, rice accounts for 22.8% of the world’s total rice cultivation area [3]. Hybrid rice cultivation has significantly increased yield to feed the large population of China [4]. If used as the main fertilizer factor to increase rice yield, N fertilizer plays an essential role in guaranteeing the high and stable rice production in China annually. The NUE in the rice fields of China is only about 30%, far lower than the world average

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