Article

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A, 107, 4477-4482

Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 02/2010; 107(9):4477-82. DOI: 10.1073/pnas.0909571107
Source: PubMed

ABSTRACT One of the most striking examples of plant developmental plasticity to changing environmental conditions is the modulation of root system architecture (RSA) in response to nitrate supply. Despite the fundamental and applied significance of understanding this process, the molecular mechanisms behind nitrate-regulated changes in developmental programs are still largely unknown. Small RNAs (sRNAs) have emerged as master regulators of gene expression in plants and other organisms. To evaluate the role of sRNAs in the nitrate response, we sequenced sRNAs from control and nitrate-treated Arabidopsis seedlings using the 454 sequencing technology. miR393 was induced by nitrate in these experiments. miR393 targets transcripts that code for a basic helix-loop-helix (bHLH) transcription factor and for the auxin receptors TIR1, AFB1, AFB2, and AFB3. However, only AFB3 was regulated by nitrate in roots under our experimental conditions. Analysis of the expression of this miR393/AFB3 module, revealed an incoherent feed-forward mechanism that is induced by nitrate and repressed by N metabolites generated by nitrate reduction and assimilation. To understand the functional role of this N-regulatory module for plant development, we analyzed the RSA response to nitrate in AFB3 insertional mutant plants and in miR393 overexpressors. RSA analysis in these plants revealed that both primary and lateral root growth responses to nitrate were altered. Interestingly, regulation of RSA by nitrate was specifically mediated by AFB3, indicating that miR393/AFB3 is a unique N-responsive module that controls root system architecture in response to external and internal N availability in Arabidopsis.

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    • "In addition to its role as a nutrient, N can act as a signal to regulate global gene expression in plants. Some specific interacting genes that respond to N treatment were identified, but very little is known about the molecular basis of N sensing and signaling, and how the transcriptomic changes result in developmental responses (Wang et al. 2003, 2004; Palenchar et al. 2004; Gutierrez et al. 2007; Vidal et al. 2010). Many reports have recently shown the relationship of nitrogen availability and resistance of plants to pathogens, but the results are so far inconsistent. "
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    • "These results confirm the existence of overlaps between auxin and SL action (Cheng et al., 2013) and the involvement of SLs in the nitrate response (Sun et al., 2014; Yoneyama et al., 2014), but also strengthen the previously hypothesized importance of TZ cells in early nitrate signalling in maize root (Manoli et al, 2014). Moreover, the identification of other components of auxin signalling, such as AUX/IAA, SAUR genes, POZ and TAZ domain-containing proteins, and an orthologue of LCR69 or LCR68, corroborate the participation of this hormone in the root response to nitrate (Vidal et al., 2010). As well as auxin and SL, brassinosteroids (BRs) also seem to belong to the network of events involved in the adaptation to nitrate fluctuations. "
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    ABSTRACT: Nitrate is an essential nutrient for plants, and crops depend on its availability for growth and development, but its presence in agricultural soils is far from stable. In order to overcome nitrate fluctuations in soil, plants have developed adaptive mechanisms allowing them to grow despite changes in external nitrate availability. Nitrate can act as both nutrient and signal, regulating global gene expression in plants, and the root tip has been proposed as the sensory organ. A set of genome-wide studies has demonstrated several nitrate-regulated genes in the roots of many plants, although only a few studies have been carried out on distinct root zones. To unravel new details of the transcriptomic and proteomic responses to nitrate availability in a major food crop, a double untargeted approach was conducted on a transition zone-enriched root portion of maize seedlings subjected to differing nitrate supplies. The results highlighted a complex transcriptomic and proteomic reprogramming that occurs in response to nitrate, emphasizing the role of this root zone in sensing and transducing nitrate signal. Our findings indicated a relationship of nitrate with biosynthesis and signalling of several phytohormones, such as auxin, strigolactones, and brassinosteroids. Moreover, the already hypothesized involvement of nitric oxide in the early response to nitrate was confirmed with the use of nitric oxide inhibitors. Our results also suggested that cytoskeleton activation and cell wall modification occurred in response to nitrate provision in the transition zone. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.
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    • "Cytokinins IPT Cytokinin biosynthesis Root branching Laplaze et al., 2007 ABA ABI4 Transcriptional regulation Root branching Shkolnik-Inbar and Bar-Zvi, 2010 Nutrient availability N AtNRT2.1 Nitrate sensing and transport Root branching Remans et al., 2006 N ANR1 Transcriptional regulation LR growth rate Zhang and Forde, 1998 N/auxin/ miR miR167a N level-dependent regulation of ARF8 mRNA level Root branching Gifford et al., 2008 N/auxin AtNRT1.1 Transport of nitrate and auxin Root branching Krouk et al., 2010 N/JA JR1 Natural alleles are associated with quantitative variation Root branching Gifford et al., 2013 N/auxin/ABA RSA1, PHO1 Natural alleles are associated with quantitative variation Root allometry Rosas et al., 2013 Signalling context Gene/protein Molecular action Main root trait(s) affected References N/miR/auxin miR393 Regulation of AFB3 mRNA abundance Root branching Vidal et al., 2010 P PDR2 "
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    ABSTRACT: Plants display a high degree of phenotypic plasticity that allows them to tune their form and function to changing environments. The plant root system has evolved mechanisms to anchor the plant and to efficiently explore soils to forage for soil resources. Key to this is an enormous capacity for plasticity of multiple traits that shape the distribution of roots in the soil. Such root system architecture-related traits are determined by root growth rates, root growth direction, and root branching. In this review, we describe how the root system is constituted, and which mechanisms, pathways, and genes mainly regulate plasticity of the root system in response to environmental variation.
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