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: 9.67). 02/2010; 107(9):4477-82. DOI: 10.1073/pnas.0909571107
Source: PubMed


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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    • "Since natural environments and agricultural fields have limited amounts of N, the production of high-yielding crops relies on the application of large quantities of nitrogenous fertilizers, which come at considerable economic (Good et al., 2004) and environmental costs (Hirel et al., 2011). The relevance of N for plants is clearly exemplified by its effects on leaf growth (von Wirén et al., 2000), senescence (Vanacker et al., 2006), root system architecture (Zhang et al., 2007; Vidal et al., 2010) and flowering time (Castro Marín et al., 2010). Besides growth and developmental effects, it is also clear that N nutrition can impact the plant's ability to cope with environmental challenges such as plant pathogen attacks (Snoeijers et al., 2000; Walters and Bingham, 2007; Dordas, 2008; Fagard et al., 2014). "
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    ABSTRACT: Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.
    Frontiers in Plant Science 11/2015; 6(142-911). DOI:10.3389/fpls.2015.00911 · 3.95 Impact Factor
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    • "TIR1 and AFB2 play more important roles during seedling development and root responses to the environment than either AFB1 or AFB3 (Parry et al., 2009). AFB3 has a unique role in the nitrate response of roots (Vidal et al., 2010), and AFB2 and AFB3 also have important roles in seed coat development (Locascio et al., 2014). AFB5 is part of an auxin receptor complex with a higher binding affinity for picloram (4-amino-3, 5, 6-trichloropicolinic acid) and specifically recognizes synthetic picolinate auxins (Walsh et al., 2006). "
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    ABSTRACT: The plant hormone auxin is a central regulator of plant growth. TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) is a component of the E3 ubiquitin ligase complex SCF(TIR1/AFB) and acts as an auxin co-receptor for nuclear auxin signaling. The SCF(TIR1/AFB)-proteasome machinery plays a central regulatory role in development-related gene transcription. Populus trichocarpa, as a model tree, has a unique fast-growth trait to which auxin signaling may contribute. However, no systematic analyses of the genome organization, gene structure, and expression of TIR1-like genes have been undertaken in this woody model plant. In this study, we identified a total of eight TIR1 genes in the Populus genome that are phylogenetically clustered into four subgroups, PtrFBL1/PtrFBL2, PtrFBL3/PtrFBL4, PtrFBL5/PtrFBL6, and PtrFBL7/PtrFBL8, representing four paralogous pairs. In addition, the gene structure and motif composition were relatively conserved in each paralogous pair and all of the PtrFBL members were localized in the nucleus. Different sets of PtrFBLs were strongly expressed in the leaves, stems, roots, cambial zones, and immature xylem of Populus. Interestingly, PtrFBL1 and 7 were expressed mainly in vascular and cambial tissues, respectively, indicating their potential but different roles in wood formation. Furthermore, Populus FBLs responded differentially upon exposure to various stresses. Finally, over-expression studies indicated a role of FBL1 in poplar stem growth and response to drought stress. Collectively, these observations lay the foundation for further investigations into the potential roles of PtrFBL genes in tree growth and development.
    Frontiers in Plant Science 10/2015; 6:126. DOI:10.3389/fpls.2015.00719 · 3.95 Impact Factor
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    • "Primary root elongation of 4-d-old maize seedlings was inhibited by treatments with 5 to 10 mM NO 3 2 for 7 d (Tian et al., 2008); primary root growth of Capsicum chinense was inhibited in 10-d-old seedlings exposed for 4 to 6 d to nitrate concentrations ranging between 0.1 and 10 mM NO 3 2 (Celis-Arámburo et al., 2011). Inhibition of primary root elongation was also observed in Arabidopsis grown either on vertical plates for 18 d on 1 mM NO 3 2 (Linkohr et al., 2002), or in a hydroponic system for 14 d and then treated for 3 d with 5 mM NO 3 2 (Vidal et al., 2010a). In addition, the dual-affinity nitrate transporter AtNPF6.3 of Arabidopsis was shown to function as a nitrate sensor involved in nitrate signaling. "

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