Abstract
BackgroundNitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified.ResultsHere we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes and functions needed to prepare plants to use or reduce nitrate. A state-space model inferred from this microarray time-series data successfully predicts gene behavior in unlearnt conditions.ConclusionsThe experiments and methods allow us to propose a temporal working model for nitrate-driven gene networks. This network model is tested both in silico and experimentally. For example, the over-expression of a predicted gene hub encoding a transcription factor induced early in the cascade indeed leads to the modification of the kinetic nitrate response of sentinel genes such as NIR, NIA2, and NRT1.1, and several other transcription factors. The potential nitrate/hormone connections implicated by this time-series data are also evaluated.
Highlights
Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development
On the SPL9 side, we found that its expression across the Affymetrix NASC dataset is either positively or negatively correlated with key molecular actors in NO3sensing, metabolism and development (NRT1.1, -0.68; NRT1.2, -0.55; ARF8, 0.73)
Our state-space model (SSM) is flexible because it enables adding unobserved variables as additional transcription factors. This systems biology study uses machine learning on time series of transcriptome data to generate testable hypotheses for the potential mechanisms underlying the NO3- transduction signal
Summary
Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. Higher plants, which constitute a main entry of nitrogen in to the food chain, acquire nitrogen mainly as nitrate (NO3-) Soil concentrations of this mineral ion can fluctuate dramatically in the rhizosphere, often resulting in limited growth and yield [1]. Data monitoring gene expression in response to NO3- provision from more than 100 Affymetrix ATH1 chips have been Despite these extensive efforts of characterization, only a limited number of molecular actors that alter NO3-induced gene regulation have been identified so far. A mutation in the NRT1.1 gene has been shown to alter plant responses to NO3- provision by changing lateral root development in NO3--rich patches of soil [15,16] and to affect control of gene expression [17,18,19,20]. Other regulatory proteins have been shown to control plant development in response to NO3- provision (such as ANR1 for lateral root development), but no evidence has so far demonstrated their role in the control of gene expression in response to NO3-
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