Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

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.

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

“…Our data indicate that the nuclear export of NLP7 slows down within minutes after the addition of nitrate, allowing a rapid NLP7-dependent regulation of gene expression. Consistent with our data, Krouk et al 9 showed that gene expression is regulated by nitrate as rapidly as 2 min after supply. …”

“…S9). The OPP pathway is a critical step providing reductants for nitrate assimilation and has been shown to have a very early response to nitrate resupply 9 . Accordingly, the list of NLP7-dependent nitrate-inducible genes includes nitrate transporter NRT2.1, nitrate reductase NIA1, nitrite reductase, glutamine synthetase 2, uroporphyrinogen III methyltransferase 1, ferredoxin 3 and transketolase (At3g60750) ( We confirmed the modified nitrate-responsive expression pattern of these genes by quantitative reverse transcription-PCR (Supplementary Figs S10 and S11).…”

Integration of responses within and acrossArabidopsisnatural accessions uncovers loci controlling root systems architecture

“…We compared the list of misregulated genes in the rsa1-1 mutant to a list of 3,186 genes regulated by the synthetic auxin naphthalene-1-acetic acid in the root (26). We found significant overrepresentations of the intersections of auxin-regulated genes with genes misregulated in the rsa1-1 mutant for both of our datasets (P < 0.001), compared with random generated gene lists of the same size (27,28), further suggesting a rsa1-1 role in auxin homeostasis. To further test whether expression of RSA1 mRNA is causative to changes in root allometry, we tested whether natural variation in RSA1 activity is correlated with changes in PC2 COL .…”

An RNA Sequencing Transcriptome Analysis Reveals Novel Insights into Molecular Aspects of the Nitrate Impact on the Nodule Activity of Medicago truncatula

“…At this point in time, nitrate application had affected the expression of 1,120 genes ($20 'unique hit' counts [DEseq] in treatment and/or controls, FDR , 0.01 and FC $ [2]). The reaction to nitrate occurred in what might be called a 'module-like' fashion, meaning that a number of genes in a dynamic and flexible gene network shifted the metabolism in a particular direction (Krouk et al, 2010a(Krouk et al, , 2010b.…”

“…A transcriptome study revealed that 550 genes were differentially expressed in the roots of this plant within 20 min after nitrate application (Krouk et al, 2010a). Estimates based on summarizing microarray data from various studies have revealed that, depending on the overall experimental context, up to approximately one-tenth of the whole genome of Arabidopsis can be influenced by the presence of nitrate (Krouk et al, 2010b).…”