Early molecular events associated with nitrogen deficiency in rice seedling roots

Ping-Han Hsieh,Ming-Hsiun Hsieh,Hsin-Yu Wu,Chia-Cheng Kan,Hsiu-Chun Yang

doi:10.1038/s41598-018-30632-1

Ping-Han Hsieh, Ming-Hsiun Hsieh + Show 3 more

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https://doi.org/10.1038/s41598-018-30632-1

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Abstract

Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (−N, 1 h), focusing on amino acid analysis and identification of −N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of −N treatment, indicating that part of the N-deficient signals could be mediated by glutamine. Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by −N. Some of the −N-regulated genes encode transcription factors, protein kinases and protein phosphatases, which may be involved in the regulation of early −N responses in rice roots. Previously, we used similar approaches to identify glutamine-, glutamate-, and ammonium nitrate-responsive genes. Comparisons of the genes induced by different forms of N with the −N-regulated genes identified here have provided a catalog of potential N regulatory genes for further dissection of the N signaling pathwys in rice.

Highlights

Rice is a staple food for almost half of the world’s population[1]
Compared with the green and healthy seedlings grown in +N hydroponic solution[36], the 10-day-old rice seedlings grown in −N medium have chlorotic leaves, thinner and longer roots (Fig. 1A)
We found that the expression of Os02g0770800 and Os08g0468100 encoding nitrate reductase (NIA), Os01g0357100 encoding nitrite reductase (NIR), Os01g0860601 encoding ferridoxin (Fd), and Os03g0784700 encoding ferredoxin-NADP reductase (FNR) was rapidly repressed by −N (Fig. 8A)

Summary

Introduction

Rice is a staple food for almost half of the world’s population[1]. The production of rice, especially in Asian countries, is important in food security. The improvement of N use efficiency in crop plants is still one of the scientific “Grand Challenges” in the 21st century To face this challenge, we need to have a better understanding of the genetics behind N uptake, transport, metabolism, and remobilization in crop plants, especially when N is limited in the environment. Microarrays were used in several studies to identify nitrate-responsive genes in Arabidopsis and rice[16,17,18,19,20,21,22]. Transcriptome analysis using microarray or RNA-Seq has been applied to identify ammonium-responsive genes in rice[23,24]. The Os02g0120100 gene encoding ACT domain-containing protein kinase 1 (ACTPK1), a homolog of Arabidopsis serine/threonine/tyrosine kinase 46 (STY46), was identified by transcriptome analysis of ammonium-responsive genes in rice roots[31]. Further genetic and biochemical studies demonstrated that ACTPK1 can phosphorylate and inactivate AMT1;2, a major ammonium transporter, under ammonium-sufficient conditions[31]

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